/var/lib/mobyle/programs/pepwheel.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
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<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>pepwheel</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>pepwheel</title>
<description>
<text lang="en">Draw a helical wheel diagram for a protein sequence</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/pepwheel.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display:protein:2D_structure</category>
<category>structure:2D_structure</category>
<command>pepwheel</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_wheel</name>
<prompt lang="en">Plot the wheel</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nowheel", "")[ bool(value) ]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>e_steps</name>
<prompt lang="en">Number of steps (value from 2 to 100)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>18</value>
</vdef>
<format>
<code proglang="python">("", " -steps=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100 is required</text>
</message>
<code proglang="python">value <= 100</code>
</ctrl>
<argpos>3</argpos>
<comment>
<text lang="en">The number of residues plotted per turn is this value divided by the 'turns' value.</text>
</comment>
</parameter>
<parameter>
<name>e_turns</name>
<prompt lang="en">Number of turns (value from 1 to 100)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="python">("", " -turns=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100 is required</text>
</message>
<code proglang="python">value <= 100</code>
</ctrl>
<argpos>4</argpos>
<comment>
<text lang="en">The number of residues plotted per turn is the 'steps' value divided by this value.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_graph</name>
<prompt lang="en">Choose the e_graph output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>png</value>
</vdef>
<vlist>
<velem>
<value>png</value>
<label>Png</label>
</velem>
<velem>
<value>gif</value>
<label>Gif</label>
</velem>
<velem>
<value>cps</value>
<label>Cps</label>
</velem>
<velem>
<value>ps</value>
<label>Ps</label>
</velem>
<velem>
<value>meta</value>
<label>Meta</label>
</velem>
<velem>
<value>data</value>
<label>Data</label>
</velem>
</vlist>
<format>
<code proglang="python">(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter>
<name>e_goutfile</name>
<prompt lang="en">Name of the output graph</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>pepwheel_graph</value>
</vdef>
<format>
<code proglang="python">("" , " -goutfile=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter isout="1">
<name>outgraph_png</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "png"</code>
</precond>
<filenames>
<code proglang="python">"*.png"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outgraph_gif</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "gif"</code>
</precond>
<filenames>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outgraph_ps</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "ps" or e_graph == "cps"</code>
</precond>
<filenames>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outgraph_meta</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "meta"</code>
</precond>
<filenames>
<code proglang="python">"*.meta"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outgraph_data</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="python">e_graph == "data"</code>
</precond>
<filenames>
<code proglang="python">"*.dat"</code>
</filenames>
</parameter>
<paragraph>
<name>e_markupsection</name>
<prompt lang="en">Markup section</prompt>
<parameters>
<parameter>
<name>e_amphipathic</name>
<prompt lang="en">Prompt for amphipathic residue marking</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -amphipathic")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'.</text>
</comment>
</parameter>
<parameter>
<name>e_squares</name>
<prompt lang="en">Mark as squares</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_amphipathic</code>
</precond>
<vdef>
<value>ILVM</value>
</vdef>
<format>
<code proglang="python">("", " -squares=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">By default the aliphatic residues ILVM are marked with squares.</text>
</comment>
</parameter>
<parameter>
<name>e_diamonds</name>
<prompt lang="en">Mark as diamonds</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_amphipathic</code>
</precond>
<vdef>
<value>DENQST</value>
</vdef>
<format>
<code proglang="python">("", " -diamonds=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">By default the residues DENQST are marked with diamonds.</text>
</comment>
</parameter>
<parameter>
<name>e_octags</name>
<prompt lang="en">Mark as octagons</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_amphipathic</code>
</precond>
<vdef>
<value>HKR</value>
</vdef>
<format>
<code proglang="python">("", " -octags=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">By default the positively charged residues HKR are marked with octagons.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>11</argpos>
</parameter>
</parameters>
</program>
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