openms_falsediscoveryrate: FalseDiscoveryRate.xml annotate

annotate FalseDiscoveryRate.xml @ 16:4138acdeedfb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:39:03 +0000
parents	6ccbf9a2072c
children

rev	line source
7 f13beb0ac55d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 3 diff changeset	1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2 <!--Proposed Tool Section: [Identification Processing]-->
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	3 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	4 <description>Estimates the false discovery rate on peptide and protein level using decoy searches</description>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <macros>
7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <import>macros.xml</import>
7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	8 </macros>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	9 <expand macro="requirements"/>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	10 <expand macro="stdio"/>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	12 @EXT_FOO@
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	13 #import re
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	14
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	15 ## Preprocessing
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	16 mkdir in &&
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	18 mkdir out &&
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	19
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	20 ## Main program call
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	21
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	22 set -o pipefail &&
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	23 @EXECUTABLE@ -write_ctd ./ &&
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	26 -in
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	28 -out
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	29 'out/output.${gxy2omsext("idxml")}'
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	30
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	31 ## Postprocessing
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	32 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	35 #end if]]></command>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	36 <configfiles>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	37 <inputs name="args_json" data_style="paths"/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	39 </configfiles>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	40 <inputs>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	41 <param argument="-in" type="data" format="idxml" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	42 <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	43 <param argument="-peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform FDR calculation on peptide level and annotates it as meta value" help="(Note: if set, also calculates FDR/q-value on PSM level.)"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	44 <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	45 <section name="FDR" title="FDR control" help="" expanded="false">
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	46 <param name="PSM" argument="-FDR:PSM" type="float" 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)"/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	47 <param name="protein" argument="-FDR:protein" type="float" 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)"/>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	48 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	49 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	50 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	51 <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"/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	52 </section>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	53 </section>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	54 <section name="algorithm" title="Parameter section for the FDR calculation algorithm" help="" expanded="false">
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	55 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	56 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	57 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	58 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	59 <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"/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	60 <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"/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	61 <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=""/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	62 </section>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	63 <expand macro="adv_opts_macro">
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	65 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	66 <expand macro="list_string_san" name="test"/>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	67 </param>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	68 </expand>
13 469690558892 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 11 diff changeset	69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
3 7e170e213707 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	71 </param>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	72 </inputs>
7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	73 <outputs>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	74 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	77 </data>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	78 </outputs>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	79 <tests>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	80 <!-- TOPP_FalseDiscoveryRate_1 -->
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	81 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	82 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	83 <param name="force" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	84 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	85 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	86 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	87 <output name="out" value="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	88 <param name="PSM" value="true"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	89 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	90 <param name="protein" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	91 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	92 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	93 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	94 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	95 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	96 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	97 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	98 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	99 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	100 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	101 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	102 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	103 <param name="split_charge_variants" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	104 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	105 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	106 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	107 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	108 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	110 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	111 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	112 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	113 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	114 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	115 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	116 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	117 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	118 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	119 <!-- TOPP_FalseDiscoveryRate_2 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	120 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	121 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	122 <param name="force" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	123 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	124 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	125 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	126 <output name="out" value="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	127 <param name="PSM" value="true"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	128 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	129 <param name="protein" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	130 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	131 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	132 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	133 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	134 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	135 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	136 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	137 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	138 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	139 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	140 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	141 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	142 <param name="split_charge_variants" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	143 <param name="treat_runs_separately" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	144 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	145 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	146 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	147 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	149 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	150 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	151 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	152 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	153 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	154 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	155 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	156 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	157 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	158 <!-- TOPP_FalseDiscoveryRate_3 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	159 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	160 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	161 <param name="force" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	162 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	163 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	164 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	165 <output name="out" value="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	166 <param name="PSM" value="true"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	167 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	168 <param name="protein" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	169 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	170 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	171 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	172 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	173 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	174 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	175 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	176 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	177 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	178 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	179 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	180 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	181 <param name="split_charge_variants" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	182 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	183 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	184 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	185 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	186 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	187 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	188 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	189 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	190 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	191 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	192 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	193 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	194 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	195 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	196 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	197 <!-- TOPP_FalseDiscoveryRate_4 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	198 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	199 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	200 <param name="force" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	201 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	202 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	203 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	204 <output name="out" value="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	205 <param name="PSM" value="true"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	206 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	207 <param name="protein" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	208 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	209 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	210 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	211 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	212 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	213 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	214 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	215 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	216 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	217 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	218 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	219 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	220 <param name="split_charge_variants" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	221 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	222 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	223 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	224 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	225 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	226 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	227 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	228 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	229 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	230 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	231 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	232 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	233 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	234 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	235 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	236 <!-- TOPP_FalseDiscoveryRate_5 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	237 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	238 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	239 <param name="force" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	240 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	241 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	242 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	243 <output name="out" value="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	244 <param name="PSM" value="false"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	245 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	246 <param name="protein" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	247 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	248 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	249 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	250 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	251 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	252 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	253 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	254 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	255 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	256 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	257 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	258 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	259 <param name="split_charge_variants" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	260 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	261 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	262 <param name="add_decoy_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	263 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	264 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	265 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	266 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	267 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	268 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	269 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	270 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	271 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	272 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	273 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	274 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	275 <!-- TOPP_FalseDiscoveryRate_6 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	276 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	277 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	278 <param name="force" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	279 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	280 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	281 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	282 <output name="out" value="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	283 <param name="PSM" value="true"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	284 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	285 <param name="protein" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	286 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	287 <param name="PSM" value="0.05"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	288 <param name="protein" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	289 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	290 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	291 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	292 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	293 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	294 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	295 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	296 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	297 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	298 <param name="split_charge_variants" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	299 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	300 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	301 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	302 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	303 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	305 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	306 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	307 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	308 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	309 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	310 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	311 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	312 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	313 </test>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	314 <!-- TOPP_FalseDiscoveryRate_7 -->
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	315 <test expect_num_outputs="2">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	316 <section name="adv_opts">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	317 <param name="force" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	318 <param name="test" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	319 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	320 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	321 <output name="out" value="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	322 <param name="PSM" value="false"/>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	323 <param name="peptide" value="false"/>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	324 <param name="protein" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	325 <section name="FDR">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	326 <param name="PSM" value="1.0"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	327 <param name="protein" value="0.3"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	328 <section name="cleanup">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	329 <param name="remove_proteins_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	330 <param name="remove_psms_without_proteins" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	331 <param name="remove_spectra_without_psms" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	332 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	333 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	334 <section name="algorithm">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	335 <param name="no_qvalues" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	336 <param name="use_all_hits" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	337 <param name="split_charge_variants" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	338 <param name="treat_runs_separately" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	339 <param name="add_decoy_peptides" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	340 <param name="add_decoy_proteins" value="false"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	341 <param name="conservative" value="true"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	342 </section>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	344 <output name="ctd_out" ftype="xml">
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	345 <assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	346 <is_valid_xml/>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	347 </assert_contents>
6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	348 </output>
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	349 <assert_stdout>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	350 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	351 </assert_stdout>
15 6ccbf9a2072c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	352 </test>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	353 </tests>
100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	354 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	355
7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	356
16 4138acdeedfb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	357 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FalseDiscoveryRate.html]]></help>
11 100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	358 <expand macro="references"/>
0 7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	359 </tool>

Mercurial > repos > galaxyp > openms_falsediscoveryrate

annotate FalseDiscoveryRate.xml @ 16:4138acdeedfb draft default tip