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author | tduigou |
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date | Wed, 21 Sep 2022 09:41:34 +0000 |
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<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09"> <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> <macros> <token name="@TOOL_VERSION@">5.13.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">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 '$adv.max_subpaths_filter' ]]></command> <inputs> <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" /> <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> <param name="sink" type="data" format="csv" label="Sink from SBML" /> <section name="adv" title="Advanced Options" expanded="false"> <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." /> <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." /> <param argument="lower_flux_bound" type="integer" value="0" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." /> </section> </inputs> <outputs> <collection name="pathways" type="list" label="${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 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ 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: * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink * **RP2paths compounds**: rp2paths compounds file * **RP2paths pathways**: rp2paths pathways file Advanced options: * **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created. * **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created. * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway. Output ------ * **pathways**: SBML completed pathways Project Links --------------------- * `GitHub <https://github.com/brsynth/rptools>`_ Version ---------- 5.13.1 Authors ------- * **Melchior du Lac** * **Joan Hérisson** Acknowledgments --------------- * Thomas Duigou Licence ------- `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ ]]></help> </tool>