Mercurial > repos > metexplore > met4j
diff build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
---|---|
date | Wed, 17 May 2023 13:26:37 +0000 |
parents | |
children | 1436e9cde9c9 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Wed May 17 13:26:37 2023 +0000 @@ -0,0 +1,119 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.3.0"> + <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> + <xrefs> + <xref type="bio.tools">met4j</xref> + </xrefs> + <requirements> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': + -cc "$colcharge" +#end if +#if str($colid) != 'nan': + -ci "$colid" +#end if + $p + $s +#if str($nSkip): + -n "$nSkip" +#end if + -sbml "$sbml" +#if str($tab) != 'None': + -tab "$tab" +#end if +#if str($c): + -c "$c" +#end if + -out "$out" +]]></command> + <inputs> + <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/> + <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> + <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/> + <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> + <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> + <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> + <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sbml" name="out"/> + </outputs> + <tests> + <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="chargesWithComment.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <param name="nSkip" value="1"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <param name="ci" value="2"/> + <param name="cc" value="3"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="sbml" value="XF_network.sbml"/> + <param name="tab" value="chargesXF.tsv"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas +The charge must be a number. The ids must correspond between the tabulated file and the SBML file. +If prefix or suffix is different in the SBML file, use the -p or the -s options. +The charge will be written in the SBML file in two locations:+ +- in the reaction notes (e.g. <p>charge: -1</p>) +- as fbc attribute (e.g. fbc:charge="1")]]></help> + <citations/> +</tool>