openms_percolatoradapter: PercolatorAdapter.xml annotate

annotate PercolatorAdapter.xml @ 9:02796e3ddec1 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 21:34:28 +0000
parents	016964c597f5
children

rev	line source
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 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.-->
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	2 <!--Proposed Tool Section: [Identification Processing]-->
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	3 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	4 <description>Facilitate input to Percolator and reintegrate</description>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	5 <macros>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	6 <token name="@EXECUTABLE@">PercolatorAdapter</token>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	7 <import>macros.xml</import>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	8 </macros>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	9 <expand macro="requirements"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	10 <expand macro="stdio"/>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	12 @EXT_FOO@
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	13 #import re
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	14
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	15 ## Preprocessing
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	16 #if $in_cond.in:
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	17 mkdir in_cond.in &&
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	18 #if $in_cond.in_select == "no"
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	20 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	21 #else
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	22 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	23 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	24 #end if
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	25 #if $in_decoy_cond.in_decoy:
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	26 mkdir in_decoy_cond.in_decoy &&
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	27 #if $in_decoy_cond.in_decoy_select == "no"
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	28 mkdir ${' '.join(["'in_decoy_cond.in_decoy/%s'" % (i) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} &&
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	29 ${' '.join(["cp '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	30 #else
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	31 cp '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' &&
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	32 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	33 #end if
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	34 #if $in_osw:
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	35 mkdir in_osw &&
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	36 cp '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	37 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	38 mkdir out &&
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	39 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	40 mkdir out_pin &&
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	41 #end if
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	42 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	43 mkdir out_pout_target &&
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	44 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	45 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	46 mkdir out_pout_decoy &&
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	47 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	48 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	49 mkdir out_pout_target_proteins &&
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	50 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	51 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	52 mkdir out_pout_decoy_proteins &&
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	53 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	54 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	55 mkdir weights &&
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	56 #end if
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	57 ## advanced options
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	58 #if $adv_opts.init_weights:
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	59 mkdir adv_opts.init_weights &&
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	60 cp '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' &&
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	61 #end if
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	62 #if $adv_opts.fasta:
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	63 mkdir adv_opts.fasta &&
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	64 cp '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' &&
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	65 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	66
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	67
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	68 ## Main program call
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	69
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	70 set -o pipefail &&
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	71 @EXECUTABLE@ -write_ctd ./ &&
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	72 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	73 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	74 #if $in_cond.in:
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	75 -in
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	76 #if $in_cond.in_select == "no"
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	77 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	78 #else
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	79 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	80 #end if
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	81 #end if
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	82 #if $in_decoy_cond.in_decoy:
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	83 -in_decoy
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	84 #if $in_decoy_cond.in_decoy_select == "no"
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	85 ${' '.join(["'in_decoy_cond.in_decoy/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	86 #else
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	87 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)'
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	88 #end if
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	89 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	90 #if $in_osw:
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	91 -in_osw
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	92 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	93 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	94 -out
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	95 'out/output.${out_type}'
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	96 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	97 -out_pin
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	98 'out_pin/output.${gxy2omsext("tabular")}'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	99 #end if
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	100 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	101 -out_pout_target
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	102 'out_pout_target/output.${gxy2omsext("tabular")}'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	103 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	104 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	105 -out_pout_decoy
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	106 'out_pout_decoy/output.${gxy2omsext("tabular")}'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	107 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	108 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	109 -out_pout_target_proteins
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	110 'out_pout_target_proteins/output.${gxy2omsext("tabular")}'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	111 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	112 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	113 -out_pout_decoy_proteins
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	114 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	115 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	116 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	117 -weights
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	118 'weights/output.${gxy2omsext("tabular")}'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	119 #end if
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	120 ## advanced options
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	121 #if $adv_opts.init_weights:
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	122 -init_weights
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	123 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)'
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	124 #end if
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	125 #if $adv_opts.fasta:
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	126 -fasta
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	127 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)'
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	128 #end if
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	129
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	130 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	131 \| tee '$stdout'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	132 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	133
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	134 ## Postprocessing
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	135 && mv 'out/output.${out_type}' '$out'
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	136 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	137 && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	138 #end if
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	139 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	140 && mv 'out_pout_target/output.${gxy2omsext("tabular")}' '$out_pout_target'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	141 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	142 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	143 && mv 'out_pout_decoy/output.${gxy2omsext("tabular")}' '$out_pout_decoy'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	144 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	145 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	146 && mv 'out_pout_target_proteins/output.${gxy2omsext("tabular")}' '$out_pout_target_proteins'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	147 #end if
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	148 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	149 && mv 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}' '$out_pout_decoy_proteins'
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	150 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	151 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	152 && mv 'weights/output.${gxy2omsext("tabular")}' '$weights'
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	153 #end if
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	154 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	155 && mv '@EXECUTABLE@.ctd' '$ctd_out'
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	156 #end if]]></command>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	157 <configfiles>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	158 <inputs name="args_json" data_style="paths"/>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	159 <configfile name="hardcoded_json"><![CDATA[{"percolator_executable": "percolator", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	160 </configfiles>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	161 <inputs>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	162 <conditional name="in_cond">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	163 <param name="in_select" type="select" label="Run tool in batch mode for -in">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	164 <option value="no">No: process all datasets jointly</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	165 <option value="yes">Yes: process each dataset in an independent job</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	166 </param>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	167 <when value="no">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	168 <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	169 </when>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	170 <when value="yes">
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	171 <param argument="-in" type="data" format="idxml,mzid" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	172 </when>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	173 </conditional>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	174 <conditional name="in_decoy_cond">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	175 <param name="in_decoy_select" type="select" label="Run tool in batch mode for -in_decoy">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	176 <option value="no">No: process all datasets jointly</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	177 <option value="yes">Yes: process each dataset in an independent job</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	178 </param>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	179 <when value="no">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	180 <param argument="-in_decoy" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	181 </when>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	182 <when value="yes">
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	183 <param argument="-in_decoy" type="data" format="idxml,mzid" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	184 </when>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	185 </conditional>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	186 <param argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	187 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	188 <option value="idXML">idxml</option>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	189 <option value="mzid">mzid</option>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	190 <option value="osw">osw</option>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	191 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	192 <expand macro="list_string_san" name="out_type"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	193 </param>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	194 <param argument="-enzyme" type="select" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help="">
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	195 <option value="no_enzyme">no_enzyme</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	196 <option value="elastase">elastase</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	197 <option value="pepsin">pepsin</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	198 <option value="proteinasek">proteinasek</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	199 <option value="thermolysin">thermolysin</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	200 <option value="chymotrypsin">chymotrypsin</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	201 <option value="lys-n">lys-n</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	202 <option value="lys-c">lys-c</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	203 <option value="arg-c">arg-c</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	204 <option value="asp-n">asp-n</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	205 <option value="glu-c">glu-c</option>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	206 <option value="trypsin" selected="true">trypsin</option>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	207 <option value="trypsinp">trypsinp</option>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	208 <expand macro="list_string_san" name="enzyme"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	209 </param>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	210 <param argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	211 <param argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	212 <param argument="-osw_level" type="select" label="OSW: the data level selected for scoring" help="">
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	213 <option value="ms1">ms1</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	214 <option value="ms2" selected="true">ms2</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	215 <option value="transition">transition</option>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	216 <expand macro="list_string_san" name="osw_level"/>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	217 </param>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	218 <param argument="-score_type" type="select" label="Type of the peptide main score" help="">
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	219 <option value="q-value" selected="true">q-value</option>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	220 <option value="pep">pep</option>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	221 <option value="svm">svm</option>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	222 <expand macro="list_string_san" name="score_type"/>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	223 </param>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	224 <expand macro="adv_opts_macro">
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	225 <param argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	226 <param argument="-subset_max_train" type="integer" value="0" label="Only train an SVM on a subset of <x> PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	227 <param argument="-cpos" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	228 <param argument="-cneg" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	229 <param argument="-testFDR" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	230 <param argument="-trainFDR" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	231 <param argument="-maxiter" type="integer" value="10" label="Maximal number of iterations" help=""/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	232 <param argument="-nested_xval_bins" type="integer" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	233 <param argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	234 <param argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	235 <param argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	236 <param argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	237 <expand macro="list_string_san" name="default_direction"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	238 </param>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	239 <param argument="-verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	240 <param argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	241 <param argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	242 <param argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	243 <param argument="-seed" type="integer" value="1" label="Setting seed of the random number generato" help=""/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	244 <param argument="-doc" type="integer" value="0" label="Include description of correct features" help=""/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	245 <param argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	246 <param argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	247 <param argument="-decoy_pattern" type="text" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help="">
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	248 <expand macro="list_string_san" name="decoy_pattern"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	249 </param>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	250 <param argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	251 <param argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	252 <param argument="-ipf_max_peakgroup_pep" type="float" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	253 <param argument="-ipf_max_transition_isotope_overlap" type="float" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	254 <param argument="-ipf_min_transition_sn" type="float" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	255 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	256 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	257 <expand macro="list_string_san" name="test"/>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	258 </param>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	259 </expand>
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	260 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	261 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	262 <option value="out_pout_target_FLAG">out_pout_target (Write pout file (e.g., for debugging))</option>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	263 <option value="out_pout_decoy_FLAG">out_pout_decoy (Write pout file (e.g., for debugging))</option>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	264 <option value="out_pout_target_proteins_FLAG">out_pout_target_proteins (Write pout file (e.g., for debugging))</option>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	265 <option value="out_pout_decoy_proteins_FLAG">out_pout_decoy_proteins (Write pout file (e.g., for debugging))</option>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	266 <option value="weights_FLAG">weights (Output final weights to the given file)</option>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	267 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	268 </param>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	269 </inputs>
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	270 <outputs>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	271 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	272 <change_format>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	273 <when input="out_type" value="mzid" format="mzid"/>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	274 <when input="out_type" value="osw" format="osw"/>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	275 </change_format>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	276 </data>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	277 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular">
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	278 <filter>OPTIONAL_OUTPUTS is not None and "out_pin_FLAG" in OPTIONAL_OUTPUTS</filter>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	279 </data>
6 147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	280 <data name="out_pout_target" label="${tool.name} on ${on_string}: out_pout_target" format="tabular">
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	281 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_FLAG" in OPTIONAL_OUTPUTS</filter>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	282 </data>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	283 <data name="out_pout_decoy" label="${tool.name} on ${on_string}: out_pout_decoy" format="tabular">
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	284 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_FLAG" in OPTIONAL_OUTPUTS</filter>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	285 </data>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	286 <data name="out_pout_target_proteins" label="${tool.name} on ${on_string}: out_pout_target_proteins" format="tabular">
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	287 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_proteins_FLAG" in OPTIONAL_OUTPUTS</filter>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	288 </data>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	289 <data name="out_pout_decoy_proteins" label="${tool.name} on ${on_string}: out_pout_decoy_proteins" format="tabular">
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	290 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_proteins_FLAG" in OPTIONAL_OUTPUTS</filter>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	291 </data>
147aaac03456 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 4 diff changeset	292 <data name="weights" label="${tool.name} on ${on_string}: weights" format="tabular">
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	293 <filter>OPTIONAL_OUTPUTS is not None and "weights_FLAG" in OPTIONAL_OUTPUTS</filter>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	294 </data>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	295 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	296 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	297 </data>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	298 </outputs>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	299 <tests>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	300 <!-- TOPP_PercolatorAdapter_1 -->
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	301 <test expect_num_outputs="2">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	302 <section name="adv_opts">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	303 <param name="generic_feature_set" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	304 <param name="subset_max_train" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	305 <param name="cpos" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	306 <param name="cneg" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	307 <param name="testFDR" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	308 <param name="trainFDR" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	309 <param name="maxiter" value="10"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	310 <param name="nested_xval_bins" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	311 <param name="quick_validation" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	312 <param name="static" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	313 <param name="default_direction" value=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	314 <param name="verbose" value="2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	315 <param name="unitnorm" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	316 <param name="test_each_iteration" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	317 <param name="override" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	318 <param name="seed" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	319 <param name="doc" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	320 <param name="klammer" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	321 <param name="decoy_pattern" value="random"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	322 <param name="post_processing_tdc" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	323 <param name="train_best_positive" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	324 <param name="ipf_max_peakgroup_pep" value="0.7"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	325 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	326 <param name="ipf_min_transition_sn" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	327 <param name="force" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	328 <param name="test" value="true"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	329 </section>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	330 <conditional name="in_cond">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	331 <param name="in" value="PercolatorAdapter_1.idXML"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	332 </conditional>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	333 <output name="out" value="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	334 <param name="out_type" value="idXML"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	335 <param name="enzyme" value="trypsin"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	336 <param name="peptide_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	337 <param name="protein_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	338 <param name="osw_level" value="ms2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	339 <param name="score_type" value="q-value"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	340 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	341 <output name="ctd_out" ftype="xml">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	342 <assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	343 <is_valid_xml/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	344 </assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	345 </output>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	346 <assert_stdout>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	347 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	348 </assert_stdout>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	349 </test>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	350 <!-- TOPP_PercolatorAdapter_2 -->
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	351 <test expect_num_outputs="2">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	352 <section name="adv_opts">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	353 <param name="generic_feature_set" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	354 <param name="subset_max_train" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	355 <param name="cpos" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	356 <param name="cneg" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	357 <param name="testFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	358 <param name="trainFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	359 <param name="maxiter" value="10"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	360 <param name="nested_xval_bins" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	361 <param name="quick_validation" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	362 <param name="static" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	363 <param name="default_direction" value=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	364 <param name="verbose" value="2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	365 <param name="unitnorm" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	366 <param name="test_each_iteration" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	367 <param name="override" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	368 <param name="seed" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	369 <param name="doc" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	370 <param name="klammer" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	371 <param name="decoy_pattern" value="random"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	372 <param name="post_processing_tdc" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	373 <param name="train_best_positive" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	374 <param name="ipf_max_peakgroup_pep" value="0.7"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	375 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	376 <param name="ipf_min_transition_sn" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	377 <param name="force" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	378 <param name="test" value="true"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	379 </section>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	380 <param name="in_osw" value="PercolatorAdapter_2.osw"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	381 <output name="out" value="PercolatorAdapter_2_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	382 <param name="out_type" value="osw"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	383 <param name="enzyme" value="trypsin"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	384 <param name="peptide_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	385 <param name="protein_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	386 <param name="osw_level" value="ms1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	387 <param name="score_type" value="q-value"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	388 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	389 <output name="ctd_out" ftype="xml">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	390 <assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	391 <is_valid_xml/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	392 </assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	393 </output>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	394 <assert_stdout>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	395 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	396 </assert_stdout>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	397 </test>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	398 <!-- TOPP_PercolatorAdapter_3 -->
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	399 <test expect_num_outputs="2">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	400 <section name="adv_opts">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	401 <param name="generic_feature_set" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	402 <param name="subset_max_train" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	403 <param name="cpos" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	404 <param name="cneg" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	405 <param name="testFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	406 <param name="trainFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	407 <param name="maxiter" value="10"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	408 <param name="nested_xval_bins" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	409 <param name="quick_validation" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	410 <param name="static" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	411 <param name="default_direction" value=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	412 <param name="verbose" value="2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	413 <param name="unitnorm" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	414 <param name="test_each_iteration" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	415 <param name="override" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	416 <param name="seed" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	417 <param name="doc" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	418 <param name="klammer" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	419 <param name="decoy_pattern" value="random"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	420 <param name="post_processing_tdc" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	421 <param name="train_best_positive" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	422 <param name="ipf_max_peakgroup_pep" value="0.7"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	423 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	424 <param name="ipf_min_transition_sn" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	425 <param name="force" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	426 <param name="test" value="true"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	427 </section>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	428 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	429 <output name="out" value="PercolatorAdapter_3_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	430 <param name="out_type" value="osw"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	431 <param name="enzyme" value="trypsin"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	432 <param name="peptide_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	433 <param name="protein_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	434 <param name="osw_level" value="ms2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	435 <param name="score_type" value="q-value"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	437 <output name="ctd_out" ftype="xml">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	438 <assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	439 <is_valid_xml/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	440 </assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	441 </output>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	442 <assert_stdout>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	443 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	444 </assert_stdout>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	445 </test>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	446 <!-- TOPP_PercolatorAdapter_4 -->
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	447 <test expect_num_outputs="2">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	448 <section name="adv_opts">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	449 <param name="generic_feature_set" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	450 <param name="subset_max_train" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	451 <param name="cpos" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	452 <param name="cneg" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	453 <param name="testFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	454 <param name="trainFDR" value="0.01"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	455 <param name="maxiter" value="10"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	456 <param name="nested_xval_bins" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	457 <param name="quick_validation" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	458 <param name="static" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	459 <param name="default_direction" value=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	460 <param name="verbose" value="2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	461 <param name="unitnorm" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	462 <param name="test_each_iteration" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	463 <param name="override" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	464 <param name="seed" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	465 <param name="doc" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	466 <param name="klammer" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	467 <param name="decoy_pattern" value="random"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	468 <param name="post_processing_tdc" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	469 <param name="train_best_positive" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	470 <param name="ipf_max_peakgroup_pep" value="0.7"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	471 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	472 <param name="ipf_min_transition_sn" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	473 <param name="force" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	474 <param name="test" value="true"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	475 </section>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	476 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	477 <output name="out" value="PercolatorAdapter_4_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	478 <param name="out_type" value="osw"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	479 <param name="enzyme" value="trypsin"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	480 <param name="peptide_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	481 <param name="protein_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	482 <param name="osw_level" value="transition"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	483 <param name="score_type" value="q-value"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	484 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	485 <output name="ctd_out" ftype="xml">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	486 <assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	487 <is_valid_xml/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	488 </assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	489 </output>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	490 <assert_stdout>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	491 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	492 </assert_stdout>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	493 </test>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	494 <!-- TOPP_PercolatorAdapter_5 -->
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	495 <test expect_num_outputs="3">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	496 <section name="adv_opts">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	497 <param name="generic_feature_set" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	498 <param name="subset_max_train" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	499 <param name="cpos" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	500 <param name="cneg" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	501 <param name="testFDR" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	502 <param name="trainFDR" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	503 <param name="maxiter" value="10"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	504 <param name="nested_xval_bins" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	505 <param name="quick_validation" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	506 <param name="static" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	507 <param name="default_direction" value=""/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	508 <param name="verbose" value="2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	509 <param name="unitnorm" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	510 <param name="test_each_iteration" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	511 <param name="override" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	512 <param name="seed" value="1"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	513 <param name="doc" value="0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	514 <param name="klammer" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	515 <param name="decoy_pattern" value="random"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	516 <param name="post_processing_tdc" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	517 <param name="train_best_positive" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	518 <param name="ipf_max_peakgroup_pep" value="0.7"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	519 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	520 <param name="ipf_min_transition_sn" value="0.0"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	521 <param name="force" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	522 <param name="test" value="true"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	523 </section>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	524 <conditional name="in_cond">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	525 <param name="in" value="PercolatorAdapter_1.idXML"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	526 </conditional>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	527 <output name="out" value="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	528 <output name="out_pin" value="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	529 <param name="out_type" value="idXML"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	530 <param name="enzyme" value="trypsin"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	531 <param name="peptide_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	532 <param name="protein_level_fdrs" value="false"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	533 <param name="osw_level" value="ms2"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	534 <param name="score_type" value="q-value"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	535 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	536 <output name="ctd_out" ftype="xml">
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	537 <assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	538 <is_valid_xml/>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	539 </assert_contents>
016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	540 </output>
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	541 <assert_stdout>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	542 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	543 </assert_stdout>
8 016964c597f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 6 diff changeset	544 </test>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	545 </tests>
e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	546 <help><![CDATA[Facilitate input to Percolator and reintegrate.
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	547
0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	548
9 02796e3ddec1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 8 diff changeset	549 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PercolatorAdapter.html]]></help>
4 e7881a82b56d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 2 diff changeset	550 <expand macro="references"/>
0 0e7bb87aa55c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: diff changeset	551 </tool>

Mercurial > repos > galaxyp > openms_percolatoradapter

annotate PercolatorAdapter.xml @ 9:02796e3ddec1 draft default tip