/var/lib/mobyle/programs/gff2ps.xml is in mobyle-programs 5.1.1-1.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>gff2ps</name>
<doc>
<title>gff2ps</title>
<description>
<text lang="en">Produces PostScript graphical output from GFF-files</text>
</description>
<authors>Josep Francesc ABRIL FERRANDO, Roderic GUIGO SERRA</authors>
<doclink>http://genome.imim.es/software/gfftools/GFF2PS.html</doclink>
</doc>
<category>display:feature_table</category>
<command>gff2ps</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>gff_file</name>
<prompt lang="en">GFF file</prompt>
<type>
<datatype>
<class>Feature</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>GFF</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>100</argpos>
</parameter>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>page_size</name>
<prompt lang="en">Modify page size (-s)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>a4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -s $value" : ""</code>
<code proglang="python">( "" , " -s "+str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>orientation</name>
<prompt lang="en">Switches page orientation to Portrait (default is Landscape) (-p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -p" : ""</code>
<code proglang="python">( "" , " -p" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>split</name>
<prompt lang="en">Sets how many pages are needed to split your output (-P)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -P $value" : ""</code>
<code proglang="python">( "" , " -P " +str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>zoom_first</name>
<prompt lang="en">Zoom first nucleotide (default is sequence origin) (-S)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -S $value" : ""</code>
<code proglang="python">( "" , " -S " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>zoom_last</name>
<prompt lang="en">Zoom last nucleotide (default is sequence length) (-E)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -E $value" : ""</code>
<code proglang="python">( "" , " -E " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>blocks</name>
<prompt lang="en">Sets blocks per page (-B)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -B $value" : ""</code>
<code proglang="python">( "" , " -B " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>nuc_per_line</name>
<prompt lang="en">Sets nucleotides per line (default is the largest sequence position from input gff-files) (-N)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -N $value" : ""</code>
<code proglang="python">( "" , " -N " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>blocks_from_left_to_right</name>
<prompt lang="en">Blocks from left to right and from top to bottom (default is top to bottom first) (-b)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -b" : ""</code>
<code proglang="python">( "" , " -b" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_headers</name>
<prompt lang="en">Switch off Header (Title area) (-L)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -L" : ""</code>
<code proglang="python">( "" , " -L" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>set_title</name>
<prompt lang="en">Defining title (default is input gff filename) (-T)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -T $value" : ""</code>
<code proglang="python">( "" , " -T " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>no_page_nb</name>
<prompt lang="en">Does not show page numbering (-l)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -l" : ""</code>
<code proglang="python">( "" , " -l" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_date</name>
<prompt lang="en">Does not show date (-O)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -O" : ""</code>
<code proglang="python">( "" , " -O" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_time</name>
<prompt lang="en">Does not show time (-o)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -o" : ""</code>
<code proglang="python">( "" , " -o" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_copyright</name>
<prompt lang="en">Switch off CopyRight line on plot (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -a" : ""</code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>color_options</name>
<prompt lang="en">Color Options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>fg_color_name</name>
<prompt lang="en">Sets color for FOREGROUND (-G)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>black</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -G $value" : ""</code>
<code proglang="python">( "" , " -G " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>bg_color_name</name>
<prompt lang="en">Sets color for BACKGROUND (-g)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>white</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -g $value" : ""</code>
<code proglang="python">( "" , " -g " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>f0_color_name</name>
<prompt lang="en">Sets color for frame 0 (-0)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>blue</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -0 $value" : ""</code>
<code proglang="python">( "" , " -0 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>f1_color_name</name>
<prompt lang="en">Sets color for frame 1 (-1)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>red</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -1 $value" : ""</code>
<code proglang="python">( "" , " -1 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>f2_color_name</name>
<prompt lang="en">Sets color for frame 2 (-2)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>green</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -2 $value" : ""</code>
<code proglang="python">( "" , " -2 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>f_color_name</name>
<prompt lang="en">Sets color for frame . (-3)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>orange</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -3 $value" : ""</code>
<code proglang="python">( "" , " -3 " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>tickmark_options</name>
<prompt lang="en">Tickmark Options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>major_tickmarks</name>
<prompt lang="en">Number of major tickmarks per line (-M)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -M $value" : ""</code>
<code proglang="python">( "" , " -M " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>major_tickmarks_scale</name>
<prompt lang="en">Major tickmarks scale in nucleotides (-K)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -K $value" : ""</code>
<code proglang="python">( "" , " -K " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default is nucleotide length for lines divided by major tickmarks number (see option -T).</text>
</comment>
</parameter>
<parameter>
<name>minor_tickmarks</name>
<prompt lang="en">Number of minor tickmarks between major tickmarks (-m)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -m $value" : ""</code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>minor_tickmarks_scale</name>
<prompt lang="en">Minor tickmarks scale in nucleotides (-k)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -k $value" : ""</code>
<code proglang="python">( "" , " -k " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default is major tickmarks size divided by minor tickmarks number (see option -t).</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>element_options</name>
<prompt lang="en">Display elements Options</prompt>
<argpos>4</argpos>
<parameters>
<parameter>
<name>no_forward_strand</name>
<prompt lang="en">Switch off displaying forward-strand(Watson) elements (-w)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -w" : ""</code>
<code proglang="python">( "" , " -w" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_reverse_strand</name>
<prompt lang="en">Switch off displaying reverse-strand(Crick) elements (-c)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -c" : ""</code>
<code proglang="python">( "" , " -c" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_strand_independent</name>
<prompt lang="en">Switch off displaying strand-independent elements (-i)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -i" : ""</code>
<code proglang="python">( "" , " -i" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_label</name>
<prompt lang="en">Switch off labels for element positions (-n)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -n" : ""</code>
<code proglang="python">( "" , " -n" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>other_options</name>
<prompt lang="en">Other Options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>default_custom_file</name>
<prompt lang="en">Create a new default customfile (-D)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -D gff2psrc" : ""</code>
<code proglang="python">( "" , " -D gff2psrc" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>user_custom_file</name>
<prompt lang="en">Your custom rc file (-C)</prompt>
<type>
<datatype>
<class>GffCustomRc</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -C $value" : ""</code>
<code proglang="python">( "" , " -C " + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Postscript output file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<format>
<code proglang="perl">"; ln -s gff2ps.out gff2ps.ps"</code>
<code proglang="python">"; ln -s gff2ps.out gff2ps.ps"</code>
</format>
<argpos>1000</argpos>
<filenames>
<code proglang="perl">"gff2ps.ps"</code>
<code proglang="python">"gff2ps.ps"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>custom_file</name>
<prompt>Custom output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$default_custom_file</code>
<code proglang="python">default_custom_file</code>
</precond>
<filenames>
<code proglang="perl">"gff2psrc"</code>
<code proglang="python">"gff2psrc"</code>
</filenames>
</parameter>
</parameters>
</program>
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