Mercurial > repos > galaxyp > openms_falsediscoveryrate

comparison FalseDiscoveryRate.xml @ 11:100359fb8e7c draft

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"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
comparison
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10:9cdf15d3cfc8 11:100359fb8e7c
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.3.0"> 4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> 5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token> 7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FalseDiscoveryRate 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_PSM: 24
22 -PSM 25 set -o pipefail &&
23 #if " " in str($param_PSM): 26 @EXECUTABLE@ -write_ctd ./ &&
24 "$param_PSM" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 $param_PSM 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #if $param_protein: 32 'out/output.${gxy2omsext("idxml")}'
30 -protein 33
31 #if " " in str($param_protein): 34 ## Postprocessing
32 "$param_protein" 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
33 #else 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 $param_protein 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #end if 38 #end if]]></command>
36 #end if 39 <configfiles>
37 #if $param_FDR_PSM: 40 <inputs name="args_json" data_style="paths"/>
38 -FDR:PSM $param_FDR_PSM 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 #if $param_FDR_protein:
41 -FDR:protein $param_FDR_protein
42 #end if
43 #if $param_algorithm_no_qvalues:
44 -algorithm:no_qvalues
45 #end if
46 #if $param_algorithm_use_all_hits:
47 -algorithm:use_all_hits
48 #end if
49 #if $param_algorithm_split_charge_variants:
50 -algorithm:split_charge_variants
51 #end if
52 #if $param_algorithm_treat_runs_separately:
53 -algorithm:treat_runs_separately
54 #end if
55 #if $param_algorithm_add_decoy_peptides:
56 -algorithm:add_decoy_peptides
57 #end if
58 #if $adv_opts.adv_opts_selector=='advanced':
59 #if $adv_opts.param_force:
60 -force
61 #end if
62 #end if
63 ]]></command>
64 <inputs> 43 <inputs>
65 <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/> 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)"/>
66 <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) "> 45 <param name="PSM" argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
67 <option value="true" selected="true">true</option> 46 <param name="protein" argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
68 <option value="false">false</option> 47 <section name="FDR" title="FDR control" help="" expanded="false">
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)"/>
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)"/>
50 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
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=""/>
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=""/>
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"/>
54 </section>
55 </section>
56 <section name="algorithm" title="Parameter section for the FDR calculation algorithm" help="" expanded="false">
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=""/>
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=""/>
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=""/>
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=""/>
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"/>
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"/>
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=""/>
64 </section>
65 <expand macro="adv_opts_macro">
66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
67 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
68 <expand macro="list_string_san"/>
69 </param>
70 </expand>
71 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
72 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
69 </param> 73 </param>
70 <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) ">
71 <option value="true" selected="true">true</option>
72 <option value="false">false</option>
73 </param>
74 <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)"/>
75 <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)"/>
76 <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) "/>
77 <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) "/>
78 <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) "/>
79 <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) "/>
80 <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"/>
81 <expand macro="advanced_options">
82 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
83 </expand>
84 </inputs> 74 </inputs>
85 <outputs> 75 <outputs>
86 <data name="param_out" format="idxml"/> 76 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
79 </data>
87 </outputs> 80 </outputs>
88 <help>Estimates the false discovery rate on peptide and protein level using decoy searches. 81 <tests>
82 <expand macro="autotest_FalseDiscoveryRate"/>
83 <expand macro="manutest_FalseDiscoveryRate"/>
84 </tests>
85 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
89 86
90 87
91 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FalseDiscoveryRate.html</help> 88 For more information, visit http://www.openms.de/documentation/TOPP_FalseDiscoveryRate.html]]></help>
89 <expand macro="references"/>
92 </tool> 90 </tool>