Mercurial > repos > galaxyp > openms_falsediscoveryrate

annotate FalseDiscoveryRate.xml @ 13:469690558892 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:34:13 +0000
parents 100359fb8e7c
children 6ccbf9a2072c
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("idxml")}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <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)"/>
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45 <param name="PSM" argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
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46 <param name="protein" argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
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47 <section name="FDR" title="FDR control" help="" expanded="false">
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48 <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)"/>
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49 <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)"/>
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50 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
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51 <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=""/>
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52 <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=""/>
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53 <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"/>
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54 </section>
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55 </section>
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56 <section name="algorithm" title="Parameter section for the FDR calculation algorithm" help="" expanded="false">
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57 <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=""/>
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58 <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=""/>
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59 <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=""/>
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60 <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=""/>
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61 <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"/>
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62 <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"/>
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63 <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=""/>
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64 </section>
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65 <expand macro="adv_opts_macro">
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66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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67 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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68 <expand macro="list_string_san"/>
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69 </param>
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70 </expand>
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71 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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72 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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73 </param>
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74 </inputs>
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75 <outputs>
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76 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <expand macro="autotest_FalseDiscoveryRate"/>
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83 <expand macro="manutest_FalseDiscoveryRate"/>
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84 </tests>
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85 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
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86
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87
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88 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FalseDiscoveryRate.html]]></help>
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89 <expand macro="references"/>
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90 </tool>