Mercurial > repos > galaxyp > openms_falsediscoveryrate
diff FalseDiscoveryRate.xml @ 11:100359fb8e7c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 12:56:39 +0000 |
parents | 7cc2a2687bff |
children | 469690558892 |
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--- a/FalseDiscoveryRate.xml Fri May 17 10:01:38 2019 -0400 +++ b/FalseDiscoveryRate.xml Wed Sep 09 12:56:39 2020 +0000 @@ -1,92 +1,90 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.3.0"> +<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> <macros> <token name="@EXECUTABLE@">FalseDiscoveryRate</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FalseDiscoveryRate + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${gxy2omsext("idxml")}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_PSM: - -PSM - #if " " in str($param_PSM): - "$param_PSM" - #else - $param_PSM - #end if -#end if -#if $param_protein: - -protein - #if " " in str($param_protein): - "$param_protein" - #else - $param_protein - #end if -#end if -#if $param_FDR_PSM: - -FDR:PSM $param_FDR_PSM -#end if -#if $param_FDR_protein: - -FDR:protein $param_FDR_protein -#end if -#if $param_algorithm_no_qvalues: - -algorithm:no_qvalues -#end if -#if $param_algorithm_use_all_hits: - -algorithm:use_all_hits -#end if -#if $param_algorithm_split_charge_variants: - -algorithm:split_charge_variants -#end if -#if $param_algorithm_treat_runs_separately: - -algorithm:treat_runs_separately -#end if -#if $param_algorithm_add_decoy_peptides: - -algorithm:add_decoy_peptides -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/> - <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> - </param> - <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> + <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/> + <param name="PSM" argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/> + <param name="protein" argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/> + <section name="FDR" title="FDR control" help="" expanded="false"> + <param name="PSM" argument="-FDR:PSM" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/> + <param name="protein" argument="-FDR:protein" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/> + <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false"> + <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/> + <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/> + <param name="remove_spectra_without_psms" argument="-FDR:cleanup:remove_spectra_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove spectra without PSMs (due to being decoy or below protein FDR threshold)" help="Caution: if remove_psms_without_proteins is false, protein level filtering does not propagate"/> + </section> + </section> + <section name="algorithm" title="Parameter section for the FDR calculation algorithm" help="" expanded="false"> + <param name="no_qvalues" argument="-algorithm:no_qvalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help=""/> + <param name="use_all_hits" argument="-algorithm:use_all_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' not only the first hit, but all are used (peptides only)" help=""/> + <param name="split_charge_variants" argument="-algorithm:split_charge_variants" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help=""/> + <param name="treat_runs_separately" argument="-algorithm:treat_runs_separately" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" help=""/> + <param name="add_decoy_peptides" argument="-algorithm:add_decoy_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy peptides will be written to output file, too" help="The q-value is set to the closest target score"/> + <param name="add_decoy_proteins" argument="-algorithm:add_decoy_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy proteins will be written to output file, too" help="The q-value is set to the closest target score"/> + <param name="conservative" argument="-algorithm:conservative" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula" help=""/> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_FDR_PSM" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter PSMs based on q-value (" help="(-PSM) e.g., 0.05 = 5% FDR, disabled for 1)"/> - <param name="param_FDR_protein" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter proteins based on q-value (" help="(-protein) e.g., 0.05 = 5% FDR, disabled for 1)"/> - <param name="param_algorithm_no_qvalues" display="radio" type="boolean" truevalue="-algorithm:no_qvalues" falsevalue="" checked="false" optional="True" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help="(-no_qvalues) "/> - <param name="param_algorithm_use_all_hits" display="radio" type="boolean" truevalue="-algorithm:use_all_hits" falsevalue="" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits) "/> - <param name="param_algorithm_split_charge_variants" display="radio" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" checked="false" optional="True" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help="(-split_charge_variants) "/> - <param name="param_algorithm_treat_runs_separately" display="radio" type="boolean" truevalue="-algorithm:treat_runs_separately" falsevalue="" checked="false" optional="True" label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" help="(-treat_runs_separately) "/> - <param name="param_algorithm_add_decoy_peptides" display="radio" type="boolean" truevalue="-algorithm:add_decoy_peptides" falsevalue="" checked="false" optional="True" label="If 'true' decoy peptides will be written to output file, too" help="(-add_decoy_peptides) The q-value is set to the closest target score"/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - </expand> </inputs> <outputs> - <data name="param_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Estimates the false discovery rate on peptide and protein level using decoy searches. + <tests> + <expand macro="autotest_FalseDiscoveryRate"/> + <expand macro="manutest_FalseDiscoveryRate"/> + </tests> + <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FalseDiscoveryRate.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FalseDiscoveryRate.html]]></help> + <expand macro="references"/> </tool>