Mercurial > repos > tduigou > rpcompletion
diff rpcompletion.xml @ 0:98d925a75257 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Tue, 23 Nov 2021 13:45:45 +0000 |
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children | b8242cf18cc0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpcompletion.xml Tue Nov 23 13:45:45 2021 +0000 @@ -0,0 +1,106 @@ +<tool id="rpCompletion" name="Complete Reactions" version="5.9.2"> + <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> + <requirements> + <requirement type="package" version="5.9.2">rptools</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" description="Could not Xref compartment_id" /> + <exit_code range="2" level="fatal" description="ValueError returned" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + python -m rptools.rpcompletion + '$rp2_pathways' + '$sink' + '$rp2paths_compounds' + '$rp2paths_pathways' + completed_pathways + --upper_flux_bound '$adv.upper_flux_bound' + --lower_flux_bound '$adv.lower_flux_bound' + --max_subpaths_filter '$adv.max_subpaths_filter' + ]]></command> + <inputs> + <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> + <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" /> + <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> + <param name="sink" type="data" format="csv" label="Sink from SBML" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" /> + <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" /> + <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" /> + </section> + </inputs> + <outputs> + <collection name="pathways" type="list" label="${tool.name}"> + <discover_datasets pattern="(?P<designation>.+)\.xml" format="xml" directory="completed_pathways" visible="false" /> + </collection> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" /> + <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" /> + <param name="rp2_pathways" value="1-rp2_metnet.csv" /> + <param name="sink" value="2-sink.csv" /> + <output_collection name="pathways" type="list"> + <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/> + <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/> + <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/> + <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/> + <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/> + <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/> + <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/> + <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/> + <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ +rpCompletion +============ + +Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. + +Input +----- + +Required: + +* **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file +* **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink +* **rp2paths_compounds**: (string) Path to the rp2paths compounds file +* **rp2paths_pathways**: (string) Path to the rp2paths pathways file +* **outdir**: (string) Path to the output directory containing sbml completed pathways + +Advanced options: + +* **-upper_flux_bound**: (integer, default=9999) Upper flux bound value +* **-lower_flux_bound**: (integer, default=0) Lower flux bound value +* **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path + +Project Links +--------------------- +* `GitHub <https://github.com/brsynth/rptools>`_ + +Version +---------- + +5.9.2 + +Authors +------- + +* **Melchior du Lac** +* **Joan Hérisson** + +Acknowledgments +--------------- + +* Thomas Duigou + +Licence +------- + +`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + + ]]></help> +</tool> \ No newline at end of file