Mercurial > repos > metexplore > met4j
comparison tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
| parents | |
| children | 9b162ee6ff8e |
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| -1:000000000000 | 0:dcd16521b969 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.11.0"> | |
| 3 <description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</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:0.11.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan': | |
| 11 -cec "$colec" | |
| 12 #end if | |
| 13 #if str($colid) != 'nan': | |
| 14 -ci "$colid" | |
| 15 #end if | |
| 16 $p | |
| 17 #if str($nSkip): | |
| 18 -n "$nSkip" | |
| 19 #end if | |
| 20 -sbml "$sbml" | |
| 21 #if str($tab) != 'None': | |
| 22 -tab "$tab" | |
| 23 #end if | |
| 24 #if str($c): | |
| 25 -c "$c" | |
| 26 #end if | |
| 27 -out "$out" | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <param argument="-cec" label="[2] number of the column where are the ecs" name="colec" optional="true" type="integer" value="2"/> | |
| 31 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> | |
| 32 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/> | |
| 33 <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"> | |
| 34 <sanitizer invalid_char="_"> | |
| 35 <valid initial="string.printable"/> | |
| 36 </sanitizer> | |
| 37 </param> | |
| 38 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/> | |
| 39 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/> | |
| 40 <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="#"> | |
| 41 <sanitizer invalid_char="_"> | |
| 42 <valid initial="string.printable"/> | |
| 43 </sanitizer> | |
| 44 </param> | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data format="sbml" name="out"/> | |
| 48 </outputs> | |
| 49 <tests> | |
| 50 <test> | |
| 51 <param name="sbml" value="toy_model.xml"/> | |
| 52 <param name="tab" value="ec.tsv"/> | |
| 53 <output ftype="sbml" name="out"> | |
| 54 <assert_contents> | |
| 55 <is_valid_xml/> | |
| 56 <has_line_matching expression=".*1.1.1.1.*" n="2"/> | |
| 57 <has_line_matching expression=".*1.2.3.4.*" n="2"/> | |
| 58 </assert_contents> | |
| 59 </output> | |
| 60 </test> | |
| 61 <test expect_failure="true"> | |
| 62 <param name="sbml" value="toy_model.xml"/> | |
| 63 <param name="tab" value="ecBad.tsv"/> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC | |
| 67 The ids must correspond between the tabulated file and the SBML file. | |
| 68 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. | |
| 69 The EC will be written in the SBML file in two locations:+ | |
| 70 - in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>) | |
| 71 - as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help> | |
| 72 </tool> |