Mercurial > repos > ggricourt > rpfbagr
changeset 0:ae38a90abb22 draft default tip
"planemo upload for repository https://github.com/brsynth/rpfbagr commit 62dcbb6831ec53f7df736c0dcbcb53e01f9c98e8-dirty"
| author | ggricourt |
|---|---|
| date | Mon, 22 Aug 2022 09:36:31 +0000 |
| parents | |
| children | |
| files | rpfbagr.xml test-data/butanol.tsv test-data/butanol.xml test-data/iAF1260.xml.gz |
| diffstat | 4 files changed, 638 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpfbagr.xml Mon Aug 22 09:36:31 2022 +0000 @@ -0,0 +1,140 @@ +<tool id="rpfbagr" name="rpfbagr" version="@TOOL_VERSION@"> + <description>Interface to predict gene knockout targets with an heterologous pathway</description> + <macros> + <token name="@TOOL_VERSION@">2.1.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rpfbagr</requirement> + </requirements> + <stdio> + <regex match="WARNING" level="warning" /> + <regex match="ERROR" level="fatal" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + python -m rpfbagr + --input-model-file '$model' + #if $pathway: + --input-pathway-file '$pathway' + #end if + #if $medium: + --input-medium-file '$medium' + #end if + --biomass-rxn-id '$biomass_rxn_id' + --target-rxn-id '$target_rxn_id' + --strategy '$input_strategy.strategy' + #if str($input_strategy.strategy) == "ko": + --substrate-rxn-id '$input_strategy.substrate_rxn_id' + #if $input_strategy.annotate: + --email "$__user_email__" + #end if + #end if + --max-knockouts '$max_knockouts' + --log-level ERROR + --output-file-tsv '$output_tsv' + ]]></command> + <inputs> + <param name="model" type="data" format="sbml" label="Chassis model file" /> + <param name="pathway" type="data" format="sbml" label="Pathway file" optional="True" /> + <param name="medium" type="data" format="tsv" label="Medium file" optional="True" /> + + <param name="biomass_rxn_id" type="text" label="Biomass reaction ID" value="" > + <validator type="empty_field" message="Biomass reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + <param name="target_rxn_id" type="text" label="Target reaction ID" value="" > + <validator type="empty_field" message="Target reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + <conditional name="input_strategy"> + <param name="strategy" type="select" label="Strategy"> + <option value="ko" selected="True">Gene knockouts</option> + <option value="ou" >Reaction knockouts</option> + </param> + <when value="ko"> + <param name="substrate_rxn_id" type="text" label="Substrate reaction ID" value="" > + <validator type="empty_field" message="Substrate reaction ID is required"/> + <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator> + </param> + <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Your email address will be used to query the NCBI website" /> + </when> + <when value="ou"> + </when> + </conditional> + <param name="max_knockouts" type="integer" value="3" min="1" max="10" label="Number of items deleted to consider" /> + </inputs> + <outputs> + <data name="output_tsv" format="tsv" label="${tool.name}(${input_strategy.strategy})" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) --> + <param name="model" value="iAF1260.xml.gz" /> + <param name="pathway" value="butanol.xml" /> + <param name="medium" value="butanol.tsv" /> + <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" /> + <param name="target_rxn_id" value="EX_1btol_e" /> + <param name="substrate_rxn_id" value="EX_glc__D_e" /> + <output name="output_tsv" > + <assert_contents> + <has_line line="reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +rpfbagr +======= + +Interface to predict gene knockout targets with an heterologous pathway. + +Input +----- + +Required: + +* **model**\ : (string) SBML file that contains chassis +* **pathway**\ : (string) SBML file that contains an heterologous pathway +* **biomass_rxn_id**\ : (string) Biomass reaction id +* **target_rxn_id**\ : (string) Reaction id to maximize +* **substrate_rxn_id**\ : (string) Substrate used +* **output_tsv**\ : (string) Path to the output file + +Strategy: + +* **strategy**\ : (string, default=ko) Strategy to apply: knockout genes or reactions + +If the strategy is to knockout genes: + +* **substrate_rxn_id**\ : (string) Substrate reaction id to use +* **email**\ : (string) Use an email adress to annotate genes with NCBI website + +Optional: + +* **medium**\ : (string) TSV file, without header, that contains medium configuration "Reaction id, lower_bound, upper_bound" +* **max_knockouts**\ : (integer, default=3) Number of items to delete in the same time + + +Project Links +--------------------- + +* `GitHub rpfbagr <https://github.com/brsynth/rpfbagr>`_ +* `Github Cameo <https://github.com/biosustain/cameo>`_ + +Authors +------- + +* **Guillaume Gricourt** + +License +------- + +MIT + ]]></help> + <citations> + <citation type="bibtex">@online{rpfbagr, + author = {BioRetroSynth group}, + title = {rpfbagr}, + url = {https://github.com/brsynth/rpfbagr}, + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.tsv Mon Aug 22 09:36:31 2022 +0000 @@ -0,0 +1,2 @@ +EX_glc__D_e -10.0 10.0 +EX_o2_e -5.0 5.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.xml Mon Aug 22 09:36:31 2022 +0000 @@ -0,0 +1,496 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="meta_butanol" id="butanol" fbc:strict="true"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> + <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> + <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <fbc:listOfObjectives fbc:activeObjective="obj"> + <fbc:objective fbc:id="obj" fbc:type="maximize"> + <fbc:listOfFluxObjectives> + <fbc:fluxObjective fbc:reaction="R_EX_1btol_e" fbc:coefficient="0.5"/> + </fbc:listOfFluxObjectives> + </fbc:objective> + </fbc:listOfObjectives> + <listOfCompartments> + <compartment id="c" name="cytosol" constant="true"/> + <compartment id="p" name="periplasm" constant="true"/> + <compartment id="e" name="extracellular space" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species metaid="meta_M_co2_e" sboTerm="SBO:0000247" id="M_co2_e" name="CO2 CO2" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="CO2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_co2_e"> + <bqbiol:is> + <rdf:Bag> + 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