Mercurial > repos > metexplore > met4j_tab2sbml
changeset 3:fb6f80555393 draft default tip
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
| author | metexplore |
|---|---|
| date | Wed, 21 Jan 2026 15:33:33 +0000 |
| parents | 1c1ec9e0ea14 |
| children | |
| files | Tab2Sbml.xml macros.xml |
| diffstat | 2 files changed, 15 insertions(+), 77 deletions(-) [+] |
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--- a/Tab2Sbml.xml Fri Nov 21 10:24:12 2025 +0000 +++ b/Tab2Sbml.xml Wed Jan 21 15:33:33 2026 +0000 @@ -12,11 +12,6 @@ #if str($colformula) != 'nan': -cf "$colformula" #end if - $rp - $mp -#if str($e): - -e "$e" -#end if #if str($i): -irr "$i" #end if @@ -27,25 +22,22 @@ #if str($id): -id "$id" #end if - $createCompartment #if str($defaultCompartment): -dcpt "$defaultCompartment" #end if + $usePalssonConvention +#if str($boundaryCompartment): + -b "$boundaryCompartment" +#end if #if str($nSkip) != 'nan': -n "$nSkip" #end if + $keepGoing -o "$sbml" ]]></command> <inputs> <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> <param argument="-cf" label="[2] number of the column where are the reaction formulas" name="colformula" optional="true" type="integer" value="2"/> - <param argument="-rp" checked="false" falsevalue="" label="[deactivated] format the reaction ids in a Palsson way (R_***)" name="rp" truevalue="-rp" type="boolean" value="false"/> - <param argument="-mp" checked="false" falsevalue="" label="[deactivated] format the metabolite ids in a Palsson way (M_***_c)" name="mp" truevalue="-mp" type="boolean" value="false"/> - <param argument="-e" label="[_b] flag to assign metabolite as external" name="e" optional="true" type="text" value="_b"> - <sanitizer invalid_char="_"> - <valid initial="string.printable"/> - </sanitizer> - </param> <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> @@ -62,78 +54,24 @@ <valid initial="string.printable"/> </sanitizer> </param> - <param argument="-cpt" checked="false" falsevalue="" label="[deactivated] Create compartment from metabolite suffixes. If this option is deactivated, only one compartment (the default compartment) will be created" name="createCompartment" truevalue="-cpt" type="boolean" value="false"/> <param argument="-dcpt" label="[c] Default compartment" name="defaultCompartment" optional="true" type="text" value="c"> <sanitizer invalid_char="_"> <valid initial="string.printable"/> </sanitizer> </param> + <param argument="-M_c" checked="false" falsevalue="" label="[false] Use Palsson et al. convention: compartment suffix in metabolite ids with _ separator" name="usePalssonConvention" truevalue="-M_c" type="boolean" value="false"/> + <param argument="-b" label="set a compartment as the system boundary. All metabolites in this compartment will have the attribute `boundaryCondition` set to true in the sbml." name="boundaryCompartment" optional="true" type="text" value=""> + <sanitizer invalid_char="_"> + <valid initial="string.printable"/> + </sanitizer> + </param> <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="integer" value="0"/> + <param argument="-ign" checked="false" falsevalue="" label="skip lines with parsing errors instead of stopping the process" name="keepGoing" truevalue="-ign" type="boolean" value="false"/> </inputs> <outputs> <data format="sbml" name="sbml"/> </outputs> - <tests> - <test> - <param name="in" value="toy_model.tsv"/> - <output ftype="sbml" name="sbml"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*reaction .*" n="7"/> - <has_line_matching expression=".*species .*" n="8"/> - </assert_contents> - </output> - </test> - <test> - <param name="in" value="toy_model_otherColumns.tsv"/> - <param name="colid" value="2"/> - <param name="colformula" value="3"/> - <output ftype="sbml" name="sbml"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*reaction .*" n="7"/> - <has_line_matching expression=".*species .*" n="8"/> - </assert_contents> - </output> - </test> - <test> - <param name="in" value="toy_model_otherSigns.tsv"/> - <param name="i" value="->"/> - <param name="r" value="="/> - <output ftype="sbml" name="sbml"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*reaction .*" n="7"/> - <has_line_matching expression=".*species .*" n="8"/> - </assert_contents> - </output> - </test> - <test> - <param name="in" value="toy_model.tsv"/> - <param name="rp" value="true"/> - <param name="mp" value="true"/> - <param name="e" value="_e"/> - <param name="createCompartment" value="true"/> - <output ftype="sbml" name="sbml"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> - <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> - <has_line_matching expression=".*id=.R_reac2.*" n="1"/> - </assert_contents> - </output> - </test> - <test> - <param name="in" value="toy_model.tsv"/> - <param name="id" value="myModel"/> - <output ftype="sbml" name="sbml"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*myModel.*" n="1"/> - </assert_contents> - </output> - </test> - </tests> + <tests/> <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas @ATTRIBUTION@]]></help> <citations/>
--- a/macros.xml Fri Nov 21 10:24:12 2025 +0000 +++ b/macros.xml Wed Jan 21 15:33:33 2026 +0000 @@ -3,7 +3,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2.0">met4j</requirement> + <requirement type="package" version="2.2.1">met4j</requirement> <yield/> </requirements> </xml> @@ -12,7 +12,7 @@ <xref type="bio.tools">met4j</xref> </xrefs> </xml> - <token name="@TOOL_VERSION@">2.2.0</token> + <token name="@TOOL_VERSION@">2.2.1</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution**