Mercurial > repos > tduigou > rpviz
diff rpviz.xml @ 0:ea2ca40a24c5 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Mon, 13 Dec 2021 17:40:42 +0000 |
parents | |
children | 8057fdd27860 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz.xml Mon Dec 13 17:40:42 2021 +0000 @@ -0,0 +1,101 @@ +<tool id="rpviz" name="Visualize pathways" version="5.10.0"> + <description>Visualize pathways from the RetroPath Suite</description> + <requirements> + <requirement type="package" version="5.10.0">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #set input_folder="input_folder" + mkdir -p '$input_folder'; + #if str($input_type_conditional.input_type) == "sbml": + #for $input in $input_type_conditional.input_sbml.keys(): + ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml'; + #end for + python -m rptools.rpviz '$input_folder' + #elif str($input_type_conditional.input_type) == "tar": + python -m rptools.rpviz '${input_type_conditional.input_tar}' + #elif str($input_type_conditional.input_type) == "single_sbml": + ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}'; + python -m rptools.rpviz '$input_folder' + #end if + 'out' + #if $adv.cofactor_file + --cofactor '$adv.cofactor_file' + #end if + --autonomous_html '$html_file'; + rm -fr '$input_folder'; + ]]></command> + <inputs> + <conditional name="input_type_conditional"> + <param name="input_type" type="select" label="Source SBML format"> + <option value="tar" selected="True">TAR</option> + <option value="sbml">Collection</option> + <option value="single_sbml">single SBML</option> + </param> + <when value="tar"> + <param name="input_tar" type="data" format="tar" label="Source SBML" /> + </when> + <when value="sbml"> + <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> + </when> + <when value="single_sbml"> + <param name="input_single_sbml" type="data" format="xml" label="Source SBML" /> + </when> + </conditional> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" /> + </section> + </inputs> + <outputs> + <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/> + </outputs> + <tests> + <test> + <!-- test 1: check if identical html output is produced (single sbml input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="single_sbml"/> + <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" /> + </conditional> + <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/> + </test> + <test> + <!-- test 2: check if identical html output is produced (tar input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="tar"/> + <param name="input_tar" value="as_tar_inputs.tgz" /> + </conditional> + <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +RPVIZ +================ +Visualize pathways from the RetroPath Suite + +Input +----- + +* **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder. + +Output +------ + +* **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised. +* **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_ + +Version +---------- + +5.10.0 + +License +------- + +* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + + ]]></help> +</tool> \ No newline at end of file