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<!-- XML Authors: bertrand Neron -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>saxs_merge</name>
<version>r17125</version>
<doc>
<title>SAXS Merge</title>
<description>
<text lang="en">Statistical merge of SAXS curves</text>
</description>
<authors>Yannick G. Spill, Seung Joong Kim, Dina Schneidman-Duhovny, Daniel
Russel, Ben Webb, Andrej Sali and Michael Nilges</authors>
</doc>
<category>protein:data:processing</category>
<command>saxs_merge.py</command>
</head>
<parameters>
<parameter ishidden="1">
<name>verbosity</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -v -v -v"</code>
<code proglang="python">" -v -v -v "</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>required</name>
<prompt lang="en">Required parameters</prompt>
<parameters>
<parameter issimple="1">
<name>stop</name>
<prompt lang="en">stop after the given step</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>merging</value>
</vdef>
<vlist>
<velem>
<label>clean up</label>
<value>cleanup</value>
</velem>
<velem>
<label>fitting</label>
<value>fitting</value>
</velem>
<velem>
<label>rescaling</label>
<value>rescaling</value>
</velem>
<velem>
<label>classification</label>
<value>classification</value>
</velem>
<velem>
<label>merging</label>
<value>merging</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " --stop=$value " : ""</code>
<code proglang="python">( "" , " --stop="+value )[value is not None and value != vdef ]</code>
</format>
<argpos>200</argpos>
</parameter>
<parameter issimple="1">
<name>postpone_cleanup</name>
<prompt lang="en">Cleanup step comes after rescaling step (default is False)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef><value>0</value></vdef>
<format>
<code proglang="perl">( $value)? " --postpone_cleanup ": ""</code>
<code proglang="python">( "" , " --postpone_cleanup ")[ value ]</code>
</format>
</parameter>
<parameter issimple="1">
<name>nb_expe</name>
<prompt lang="en">Number of times each profile has been recorded</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<ctrl>
<message>
<text lang="en">the number of recordings must be > 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>11</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>SAXS</name>
<prompt lang="en">SAXS profile</prompt>
<type>
<datatype>
<class>MultipleIntensity</class>
<superclass>MultipleAbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined value)? "$value=$nb_expe_1" : ""</code>
<code proglang="python">" ".join([ "%s=%d"%(v, nb_expe) for v in value.split(" ")])</code>
</format>
<argpos>10</argpos>
<separator> </separator>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>advanced</name>
<prompt>Advanced parameters</prompt>
<parameters>
<paragraph>
<name>advanced_general</name>
<prompt lang="en">General</prompt>
<parameters>
<parameter>
<name>general_header</name>
<prompt lang="en">First line of output files is a header</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " --header "":""</code>
<code proglang="python">( "" , " --header ")[ value ]</code>
</format>
</parameter>
<parameter>
<name>allfiles</name>
<prompt lang="en">Output data files for parsed input files as well.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " --allfiles "":""</code>
<code proglang="python">( "" , " --allfiles ")[ value ]</code>
</format>
</parameter>
<parameter>
<name>outlevel</name>
<prompt lang="en">Set the output level</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>normal</value>
</vdef>
<vlist>
<velem>
<label>sparse</label>
<value>sparse</value>
</velem>
<velem>
<label>normal</label>
<value>normal</value>
</velem>
<velem>
<label>full</label>
<value>full</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value neq $vdef) " --outlevel=$value"":""</code>
<code proglang="python">( "" , " --outlevel="+value)[ value is not None and value != vdef]</code>
</format>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<ul>
<li>'sparse' is for q,I,err columns</li>
<li>'normal' adds eorigin, eoriname and eextrapol (default)</li>
<li>'full' outputs all flag</li>
</ul>
</div>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>advanced_cleanup</name>
<prompt lang="en">Cleanup (Step 1)</prompt>
<parameters>
<parameter>
<name>aalpha</name>
<prompt lang="en">type I error (default 1e-4)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1e-4</value>
</vdef>
<ctrl>
<message>
<text lang="en">must be >= 0 and <=1</text>
</message>
<code proglang="perl">$value>= 0 && $value <=1 </code>
<code proglang="python">value>= 0 and value <=1 </code>
</ctrl>
<format>
<code proglang="perl">(defined $value and value != $vdef )" --aalpha=$value":""</code>
<code proglang="python">( "" , " --aalpha="+str(value))[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en"> Discard or keep SAXS curves' points based on their SNR.
Points with an error of zero are discarded as well
</text>
</comment>
</paragraph>
<paragraph>
<name>advanced_fitting</name>
<prompt lang="en">Fitting (Step 2)</prompt>
<parameters>
<parameter>
<name>bmean</name>
<prompt lang="en">bmean</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Full</value>
</vdef>
<vlist>
<velem>
<label>Flat</label>
<value>Flat</value>
</velem>
<velem>
<label>Simple</label>
<value>Simple</value>
</velem>
<velem>
<label>Generalized</label>
<value>Generalized</value>
</velem>
<velem>
<label>Full</label>
<value>Full</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and value neq $vdef)? " --bmean=$value ": "" </code>
<code proglang="python">("" , " --bmean="+str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
Defines the most complex mean function that will be tried during model comparison.
<ul>
<li>One of Flat (the offset parameter A is optimized)</li>
<li>Simple (optimizes A, G and Rg)</li>
<li>Generalized (optimizes G, Rg and d)</li>
<li>Full (optimizes G, Rg, d and s) If "Don't perform model comparison" is set,
will try to fit only with this model.</li>
</ul>
</div>
</comment>
</parameter>
<parameter>
<name>bnocomp</name>
<prompt lang="en">perform model comparison</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value)? "": " --bnocomp "</code>
<code proglang="python">( " --bnocomp " ,"" )[ value is not None and value != vdef ]</code>
</format>
</parameter>
<parameter>
<name>berror</name>
<prompt lang="en">berror: Compute error bars on all parameters even in case where model comparison was disabled.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef><value>1</value></vdef>
<format>
<code proglang="perl">(defined $value)? " --berror " : ""</code>
<code proglang="python">( "" , " --berror ")[ value ]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>blimit_fitting</name>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>80</value>
</vdef>
<format>
<code proglang="perl">" --blimit_fitting=$value "</code>
<code proglang="python">" --blimit_fitting=%d "%(value)</code>
</format>
</parameter>
<parameter ishidden="1">
<name>blimit_hessian</name>
<prompt lang="en">set the maximum number of points used in the Hessian calculation.</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>80</value>
</vdef>
<format>
<code proglang="perl">" --blimit_hessian=$value "</code>
<code proglang="python">" --blimit_hessian=%d "%(value)</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en">To save resources, set the maximum number of points
used in the Hessian calculation (model comparison,
options baverage, and berror ). Dataset will be
subsampled if it is bigger than NUM. If NUM=-1
(default), all points will be used.</text>
</comment>
</paragraph>
<paragraph>
<name>advanced_rescaling</name>
<prompt lang="en">Rescaling (Step 3)</prompt>
<parameters>
<parameter>
<name>cmodel</name>
<prompt lang="en">Which rescaling model to use to calculate gamma.</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>normal</value>
</vdef>
<vlist>
<velem>
<label>normal</label>
<value>normal</value>
</velem>
<velem>
<label>normal-offset</label>
<value>normal-offset</value>
</velem>
<velem>
<label>lognormal</label>
<value>lognormal</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " --cmodel=$value ": ""</code>
<code proglang="python">( "" , " --cmodel="+str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
<ul>
<li>'normal-offset' for a normal model with offset,</li>
<li>'normal' (default) for a normal model with zero offset,</li>
<li>and 'lognormal' for a lognormal model.</li>
</ul>
</div>
</comment>
</parameter>
</parameters>
<comment>
<text lang="en">Find the most probable scaling factor of all curves wrt the first curve.</text>
</comment>
</paragraph>
<paragraph>
<name>advanced_classification</name>
<prompt lang="en">Classification (Step 4)</prompt>
<parameters>
<parameter>
<name>dalpha</name>
<prompt lang="en">type I error (default 0.05)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.05</value>
</vdef>
<ctrl>
<message>
<text lang="en">must be >= 0 and <=1</text>
</message>
<code proglang="perl">$value>= 0 && $value <=1 </code>
<code proglang="python">value>= 0 and value <=1 </code>
</ctrl>
<format>
<code proglang="perl">(defined $value and $value != $vdef) " --dalpha=$value " : ""</code>
<code proglang="python">( "" , " --dalpha="+str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en">Classify the mean curves by comparing them using a two-sided two-sample student t test</text>
</comment>
</paragraph>
<paragraph>
<name>advanced_merging</name>
<prompt lang="en">Merging (Step 5)</prompt>
<parameters>
<parameter>
<name>emean</name>
<prompt lang="en">Which most complex mean function to try for model comparison.</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Full</value>
</vdef>
<vlist>
<velem>
<label>Flat</label>
<value>Flat</value>
</velem>
<velem>
<label>Simple</label>
<value>Simple</value>
</velem>
<velem>
<label>Generalized</label>
<value>Generalized</value>
</velem>
<velem>
<label>Full</label>
<value>Full</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and value neq $vdef)? " --emean=$value ": "" </code>
<code proglang="python">("" , " --emean="+str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<div xmlns="http://www.w3.org/1999/xhtml">
Which mean parameters are optimized.
<ul>
<li>One of Flat (the offset parameter A is optimized)</li>
<li>Simple (optimizes A, G and Rg)</li>
<li>Generalized (default, optimizes G, Rg and d)</li>
<li>Full (optimizes G, Rg, d and s)</li>
</ul>
</div>
</comment>
</parameter>
<parameter>
<name>enocomp</name>
<prompt lang="en">perform model comparison</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value)? "": " --enocomp "</code>
<code proglang="python">( " --enocomp " , "")[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Perform model comparison, which allows to choose a
mean function that does not overfit the data. If
ecomp is given, eoptimize is taken to be the most
complex model. (Default: don't perform it.)</text>
</comment>
</parameter>
<parameter>
<name>eerror</name>
<prompt lang="en">Compute error bars on all parameters even in case where model comparison was disabled.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef><value>1</value></vdef>
<format>
<code proglang="perl">(defined $value)? " --eerror " : ""</code>
<code proglang="python">( "" , " --eerror ")[ value ]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>elimit_fitting</name>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>80</value>
</vdef>
<format>
<code proglang="perl">" --elimit_fitting=$value "</code>
<code proglang="python">" --elimit_fitting=%d "%(value)</code>
</format>
</parameter>
<parameter ishidden="1">
<name>elimit_hessian</name>
<prompt lang="en">Set the maximum number of points used in the Hessian calculation</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>80</value>
</vdef>
<format>
<code proglang="perl">" --elimit_hessian=$value "</code>
<code proglang="python">" --elimit_hessian=%d "% value</code>
</format>
</parameter>
<parameter>
<name>enoextrapolate</name>
<prompt lang="en"> Don't extrapolate at all, even at low angle.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(value?) " --enoextrapolate ": ""</code>
<code proglang="python">( "" , " --enoextrapolate ")[value]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en">Find the most probable scaling factor of all curves wrt the first</text>
</comment>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>expert</name>
<prompt lang="en">Expert parameters</prompt>
<parameters>
<paragraph>
<name>advanced_general</name>
<prompt lang="en">General</prompt>
<parameters>
<parameter>
<name>use_npoints</name>
<prompt lang="en">Skip next option and use q values of the first datafile instead.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef><value>0</value></vdef>
</parameter>
<parameter>
<name>npoints</name>
<prompt>Number of points to output for the mean function.</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef><value>200</value></vdef>
<format>
<code proglang="perl">($use_npoints and $value > 0)? " --npoints=$value ": " --npoints=-1 "</code>
<code proglang="python">( " --npoints=-1 " , " --npoints="+str(value) )[use_npoints and value > 0]</code>
</format>
</parameter>
<parameter>
<name>lambdamin</name>
<prompt lang="en">lower bound for lambda parameter in steps 2 and 5</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef><value>0.005</value></vdef>
<format>
<code proglang="python">(defined $value and $value != $vdef)?" --lambdamin=$value ":""</code>
<code proglang="python">( "" , " --lambdamin="+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>expert_cleanup</name>
<prompt lang="en">Cleanup (Step 1)</prompt>
<parameters>
<parameter>
<name>acutof</name>
<prompt lang="en">when a value after CUT is discarded, the rest of the curve is discarded as well (default is 0.1)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --acutoff=$value " : ""</code>
<code proglang="python">( "" , " --acutoff="+str(value))[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en"> Discard or keep SAXS curves' points based on their SNR.
Points with an error of zero are discarded as well
</text>
</comment>
</paragraph>
<paragraph>
<name>expert_fitting</name>
<prompt lang="en">Fitting (Step 2)</prompt>
<parameters>
<parameter>
<name>baverage</name>
<prompt lang="en">baverage: Average over all possible parameters instead of just
taking the most probable set of parameters.
</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --baverage ": ""</code>
<code proglang="python">( "" , " --baverage ")[ value is not None and value!= vdef ]</code>
</format>
</parameter>
<parameter>
<name>bd</name>
<prompt lang="en">Initial value for d</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<ctrl>
<message>
<text lang="en">must be greater than 0</text>
</message>
<code proglang="perl">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --bd=$value":""</code>
<code proglang="python">( "", " --bd="+str(value))[ value is not None and value != vdef ]</code>
</format>
</parameter>
<parameter>
<name>bs</name>
<prompt lang="en">Initial value for s</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<ctrl>
<message>
<text lang="en">must be greater or equal than 0</text>
</message>
<code proglang="perl">$value >= 0</code>
<code proglang="python">value >= 0</code>
</ctrl>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --bs=$value":""</code>
<code proglang="python">( "", " --bs="+str(value))[ value is not None and value != vdef ]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en">Estimate the mean function and the noise level of each SAXS curve.</text>
</comment>
</paragraph>
<paragraph>
<name>expert_rescaling</name>
<prompt lang="en">Rescaling (Step 3)</prompt>
<parameters>
<parameter>
<name>creference</name>
<prompt lang="en">Define which input curve the other curves will be recaled to.</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>last</value>
</vdef>
<vlist>
<velem>
<label>last</label>
<value>last</value>
</velem>
<velem>
<label>first</label>
<value>first</value>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value != vdef) " --creference=$value" : ""</code>
<code proglang="python">( "" , " --creference="+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>cnpoints</name>
<prompt lang="en">Number of points to use to compute gamma (default 200)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != vdef)? " --cnpoints=$value ":""</code>
<code proglang="python">( "", " --cnpoints="+str(value))[value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
<comment>
<text lang="en">Find the most probable scaling factor of all curves wrt the first</text>
</comment>
</paragraph>
<paragraph>
<name>expert_merging</name>
<prompt lang="en">Merging (Step 5)</prompt>
<parameters>
<parameter>
<name>eaverage</name>
<prompt lang="en">Average over all possible parameters instead of just
taking the most probable set of parameters.
</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --eaverage ": ""</code>
<code proglang="python">( "" , " --eaverage ")[ value is not None and value!= vdef ]</code>
</format>
</parameter>
<parameter>
<name>eextrapolate</name>
<prompt lang="en">Extrapolate NUM percent outside of the curve's bounds.</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " --eextrapolate=$value":""</code>
<code proglang="python">( "", " --eextrapolate="+str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Example: if NUM=50 and the highest acceptable data
point is at q=0.3, the mean will be estimated up to q=0.45.
Default is 0 (just extrapolate at low angle).
</text>
</comment>
</parameter>
</parameters>
<comment>
<text lang="en">Collect compatible data and produce best estimate of mean function.</text>
</comment>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>sparse_output</name>
<prompt lang="en">Output</prompt>
<precond>
<code proglang="perl">outlevel eq "sparse"</code>
<code proglang="python">outlevel == "sparse"</code>
</precond>
<parameters>
<parameter isout="1">
<name>sparse_summary</name>
<prompt lang="en">Report</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"summary.txt"</code>
<code proglang="python">"summary.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>sparse_merge</name>
<prompt lang="en">Merged data</prompt>
<type>
<datatype>
<class>SAXSMerge</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"data_merged.dat"</code>
<code proglang="python">"data_merged.dat"</code>
</filenames>
<comment>
<text lang="en">selection de données d'entrées 3 cols q i err</text>
</comment>
</parameter>
<parameter isout="1">
<name>sparse_mean</name>
<prompt lang="en">Interpolation</prompt>
<type>
<datatype>
<class>SAXSIntepolation</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"mean_merged.dat"</code>
<code proglang="python">"mean_merged.dat"</code>
</filenames>
<comment>
<text lang="en">interpolation 3 cols q i err</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>normal_output</name>
<prompt lang="en">Output</prompt>
<precond>
<code proglang="perl">outlevel eq "normal"</code>
<code proglang="python">outlevel == "normal"</code>
</precond>
<parameters>
<parameter isout="1">
<name>normal_summary</name>
<prompt lang="en">Report</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"summary.txt"</code>
<code proglang="python">"summary.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>normal_merge</name>
<prompt lang="en">Merged data</prompt>
<type>
<datatype>
<class>SAXSMerge</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"data_merged.dat"</code>
<code proglang="python">"data_merged.dat"</code>
</filenames>
<comment>
<text lang="en">selection de données d'entrées q i err eorigin eoriname eextrapol</text>
</comment>
</parameter>
<parameter isout="1">
<name>normal_mean</name>
<prompt lang="en">Interpolation</prompt>
<type>
<datatype>
<class>SAXSIntepolation</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"mean_merged.dat"</code>
<code proglang="python">"mean_merged.dat"</code>
</filenames>
<comment>
<text lang="en">interpolation q i err eorigin eoriname eextrapol</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>full_output</name>
<prompt lang="en">Output</prompt>
<precond>
<code proglang="perl">outlevel eq "full"</code>
<code proglang="python">outlevel == "full"</code>
</precond>
<parameters>
<parameter isout="1">
<name>full_summary</name>
<prompt lang="en">Report</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"summary.txt"</code>
<code proglang="python">"summary.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>full_merge</name>
<prompt lang="en">Merged data</prompt>
<type>
<datatype>
<class>SAXSMerge</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"data_merged.dat"</code>
<code proglang="python">"data_merged.dat"</code>
</filenames>
<comment>
<text lang="en">q i err eorigin eoriname eextrapol</text>
</comment>
</parameter>
<parameter isout="1">
<name>full_mean</name>
<prompt lang="en">Interpolation</prompt>
<type>
<datatype>
<class>SAXSIntepolation</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"mean_merged.dat"</code>
<code proglang="python">"mean_merged.dat"</code>
</filenames>
<comment>
<text lang="en">q i err eorigin eoriname eextrapol</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>all_files_output</name>
<prompt lang="en">Output</prompt>
<precond>
<code proglang="perl">allfiles</code>
<code proglang="python">allfiles</code>
</precond>
<parameters>
<parameter isout="1">
<name>all_file_data</name>
<prompt lang="en">Merged data</prompt>
<type>
<datatype>
<class>SAXSMerge</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"data_*"</code>
<code proglang="python">"data_*"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>all_files_mean</name>
<prompt lang="en">Interpolation</prompt>
<type>
<datatype>
<class>SAXSIntepolation</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"mean_*"</code>
<code proglang="python">"mean_*"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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