Mercurial > repos > metexplore > met4j
comparison 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 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.3.0"> | |
| 3 <description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': | |
| 11 -cc "$colcharge" | |
| 12 #end if | |
| 13 #if str($colid) != 'nan': | |
| 14 -ci "$colid" | |
| 15 #end if | |
| 16 $p | |
| 17 $s | |
| 18 #if str($nSkip): | |
| 19 -n "$nSkip" | |
| 20 #end if | |
| 21 -sbml "$sbml" | |
| 22 #if str($tab) != 'None': | |
| 23 -tab "$tab" | |
| 24 #end if | |
| 25 #if str($c): | |
| 26 -c "$c" | |
| 27 #end if | |
| 28 -out "$out" | |
| 29 ]]></command> | |
| 30 <inputs> | |
| 31 <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/> | |
| 32 <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/> | |
| 33 <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"/> | |
| 34 <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"/> | |
| 35 <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"> | |
| 36 <sanitizer invalid_char="_"> | |
| 37 <valid initial="string.printable"/> | |
| 38 </sanitizer> | |
| 39 </param> | |
| 40 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> | |
| 41 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> | |
| 42 <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="#"> | |
| 43 <sanitizer invalid_char="_"> | |
| 44 <valid initial="string.printable"/> | |
| 45 </sanitizer> | |
| 46 </param> | |
| 47 </inputs> | |
| 48 <outputs> | |
| 49 <data format="sbml" name="out"/> | |
| 50 </outputs> | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="sbml" value="toy_model.xml"/> | |
| 54 <param name="tab" value="charges.tsv"/> | |
| 55 <output ftype="sbml" name="out"> | |
| 56 <assert_contents> | |
| 57 <is_valid_xml/> | |
| 58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> | |
| 59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> | |
| 60 </assert_contents> | |
| 61 </output> | |
| 62 </test> | |
| 63 <test> | |
| 64 <param name="sbml" value="toy_model.xml"/> | |
| 65 <param name="tab" value="chargesWithComment.tsv"/> | |
| 66 <output ftype="sbml" name="out"> | |
| 67 <assert_contents> | |
| 68 <is_valid_xml/> | |
| 69 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> | |
| 70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> | |
| 71 </assert_contents> | |
| 72 </output> | |
| 73 </test> | |
| 74 <test> | |
| 75 <param name="sbml" value="toy_model.xml"/> | |
| 76 <param name="tab" value="charges.tsv"/> | |
| 77 <param name="nSkip" value="1"/> | |
| 78 <output ftype="sbml" name="out"> | |
| 79 <assert_contents> | |
| 80 <is_valid_xml/> | |
| 81 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> | |
| 82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> | |
| 83 </assert_contents> | |
| 84 </output> | |
| 85 </test> | |
| 86 <test> | |
| 87 <param name="sbml" value="toy_model.xml"/> | |
| 88 <param name="tab" value="charges.tsv"/> | |
| 89 <param name="ci" value="2"/> | |
| 90 <param name="cc" value="3"/> | |
| 91 <output ftype="sbml" name="out"> | |
| 92 <assert_contents> | |
| 93 <is_valid_xml/> | |
| 94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> | |
| 95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> | |
| 96 </assert_contents> | |
| 97 </output> | |
| 98 </test> | |
| 99 <test> | |
| 100 <param name="sbml" value="XF_network.sbml"/> | |
| 101 <param name="tab" value="chargesXF.tsv"/> | |
| 102 <param name="p" value="true"/> | |
| 103 <param name="s" value="true"/> | |
| 104 <output ftype="sbml" name="out"> | |
| 105 <assert_contents> | |
| 106 <is_valid_xml/> | |
| 107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> | |
| 108 </assert_contents> | |
| 109 </output> | |
| 110 </test> | |
| 111 </tests> | |
| 112 <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas | |
| 113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file. | |
| 114 If prefix or suffix is different in the SBML file, use the -p or the -s options. | |
| 115 The charge will be written in the SBML file in two locations:+ | |
| 116 - in the reaction notes (e.g. <p>charge: -1</p>) | |
| 117 - as fbc attribute (e.g. fbc:charge="1")]]></help> | |
| 118 <citations/> | |
| 119 </tool> |