Mercurial > repos > tduigou > rp2biosensor
diff rp2biosensor.xml @ 1:b7713d32248b draft
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author | tduigou |
---|---|
date | Fri, 25 Feb 2022 07:16:18 +0000 |
parents | eaab33f23abf |
children | b0efd4b2ffba |
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--- a/rp2biosensor.xml Wed Jan 05 16:14:32 2022 +0000 +++ b/rp2biosensor.xml Fri Feb 25 07:16:18 2022 +0000 @@ -1,24 +1,36 @@ -<tool id="rp2biosensor" name="rp2biosensor" version="1.0.1"> +<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09"> <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description> + <macros> + <token name="@TOOL_VERSION@">2.1.0</token> + </macros> <requirements> - <requirement type="package" version="1.0.1">rp2biosensor</requirement> + <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python -m rp2biosensor '$rp2_results' --opath '$html_file' + #if str($adv.json_graph) == "true" + --ojson '$json_file' + #end if ]]></command> <inputs> <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" /> + </section> </inputs> <outputs> <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/> + <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}"> + <filter> adv['json_graph'] </filter> + </data> </outputs> <tests> <test> <!-- test 1: check if identical outputs are produced --> - <param name="rp2_results" value="rp2-results_dmax-16.csv" /> - <output name="html_file" md5="4abb29e769106e75e68a939764dd2e31"/> + <param name="rp2_results" value="rp2-results-lactate.csv" /> + <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/> </test> </tests> <help><![CDATA[ @@ -39,7 +51,9 @@ * **opath**\ : (string) Output path. Default: biosensor.html. -* **o_sbol_dir**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file. +* **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file. + +* **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None Project Links ------------------ @@ -49,7 +63,7 @@ Version ---------- -1.0.1 +2.1.0 Authors -------