openms_idfileconverter: IDFileConverter.xml annotate

annotate IDFileConverter.xml @ 16:5e9c35b8d194 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 21:43:27 +0000
parents	7d0eb300f360
children

rev	line source
7 1dcffdad49c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 3 diff changeset	1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2 <!--Proposed Tool Section: [File Converter]-->
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	3 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	4 <description>Converts identification engine file formats</description>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <macros>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <token name="@EXECUTABLE@">IDFileConverter</token>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <import>macros.xml</import>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	8 </macros>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	9 <expand macro="requirements"/>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	10 <expand macro="stdio"/>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	12 @EXT_FOO@
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	13 #import re
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	14
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	15 ## Preprocessing
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	16 mkdir in &&
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	18 mkdir out &&
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	19 #if $mz_file:
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	20 mkdir mz_file &&
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	21 cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
3 066cf4d993f5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 2 diff changeset	22 #end if
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	23
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	24 ## Main program call
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	25
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	26 set -o pipefail &&
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	27 @EXECUTABLE@ -write_ctd ./ &&
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	30 -in
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	32 -out
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	33 'out/output.${out_type}'
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	34 #if $mz_file:
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	35 -mz_file
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	36 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)'
7 1dcffdad49c0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 3 diff changeset	37 #end if
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	38
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	39 ## Postprocessing
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	40 && mv 'out/output.${out_type}' '$out'
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	41 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	42 && mv '@EXECUTABLE@.ctd' '$ctd_out'
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	43 #end if]]></command>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	44 <configfiles>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	45 <inputs name="args_json" data_style="paths"/>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	47 </configfiles>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	48 <inputs>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	49 <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" label="Input file or directory containing the data to convert" help="This may be:. - a single file in OpenMS database format (.oms),. - a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single file in fasta format (can only be used to generate a theoretical mzML),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files.. select fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml data sets(s)"/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	50 <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	51 <option value="fasta">fasta</option>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	52 <option value="idXML">idxml</option>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	53 <option value="mzML">mzml</option>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	54 <option value="mzid">mzid</option>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	55 <option value="oms">sqlite (oms)</option>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	56 <option value="pepXML">pepxml</option>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	57 <option value="xquest.xml">xquest.xml</option>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	58 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	59 <expand macro="list_string_san" name="out_type"/>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	60 </param>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	61 <param argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	62 <param argument="-mz_name" type="text" optional="true" value="" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="Only necessary if different from 'mz_file'">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	63 <expand macro="list_string_san" name="mz_name"/>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	64 </param>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	65 <param argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	66 <param argument="-score_type" type="select" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	67 <option value="qvalue" selected="true">qvalue</option>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	68 <option value="PEP">PEP</option>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	69 <option value="score">score</option>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	70 <expand macro="list_string_san" name="score_type"/>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	71 </param>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	72 <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	73 <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	74 <option value="none" selected="true">none</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	75 <option value="coarse">coarse</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	76 <option value="fine">fine</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	77 <expand macro="list_string_san" name="isotope_model"/>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	78 </param>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	79 <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	80 <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	81 <param name="add_metainfo" argument="-fasta_to_mzml:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	82 <param name="add_losses" argument="-fasta_to_mzml:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	83 <param name="sort_by_position" argument="-fasta_to_mzml:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	84 <param name="add_precursor_peaks" argument="-fasta_to_mzml:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	85 <param name="add_all_precursor_charges" argument="-fasta_to_mzml:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	86 <param name="add_abundant_immonium_ions" argument="-fasta_to_mzml:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	87 <param name="add_first_prefix_ion" argument="-fasta_to_mzml:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	88 <param name="add_y_ions" argument="-fasta_to_mzml:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	89 <param name="add_b_ions" argument="-fasta_to_mzml:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	90 <param name="add_a_ions" argument="-fasta_to_mzml:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	91 <param name="add_c_ions" argument="-fasta_to_mzml:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	92 <param name="add_x_ions" argument="-fasta_to_mzml:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	93 <param name="add_z_ions" argument="-fasta_to_mzml:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	94 <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	95 <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	96 <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	97 <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	98 <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	99 <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	100 <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	101 <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	102 <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	103 <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	104 <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" label="Enzym used to digest the fasta proteins" help="">
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	105 <option value="Trypsin" selected="true">Trypsin</option>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	106 <option value="Arg-C">Arg-C</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	107 <option value="no cleavage">no cleavage</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	108 <option value="unspecific cleavage">unspecific cleavage</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	109 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	110 <option value="Glu-C+P">Glu-C+P</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	111 <option value="PepsinA + P">PepsinA + P</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	112 <option value="cyanogen-bromide">cyanogen-bromide</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	113 <option value="Clostripain/P">Clostripain/P</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	114 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	115 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	116 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	117 <option value="2-iodobenzoate">2-iodobenzoate</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	118 <option value="iodosobenzoate">iodosobenzoate</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	119 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	120 <option value="Trypsin/P">Trypsin/P</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	121 <option value="V8-DE">V8-DE</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	122 <option value="Arg-C/P">Arg-C/P</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	123 <option value="Asp-N">Asp-N</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	124 <option value="Asp-N/B">Asp-N/B</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	125 <option value="Asp-N_ambic">Asp-N_ambic</option>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	126 <option value="Chymotrypsin">Chymotrypsin</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	127 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	128 <option value="CNBr">CNBr</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	129 <option value="Formic_acid">Formic_acid</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	130 <option value="Lys-C">Lys-C</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	131 <option value="Lys-N">Lys-N</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	132 <option value="Lys-C/P">Lys-C/P</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	133 <option value="PepsinA">PepsinA</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	134 <option value="TrypChymo">TrypChymo</option>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	135 <option value="V8-E">V8-E</option>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	136 <option value="leukocyte elastase">leukocyte elastase</option>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	137 <option value="proline endopeptidase">proline endopeptidase</option>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	138 <expand macro="list_string_san" name="enzyme"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	139 </param>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	140 <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	141 <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" value="1" label="Minimum charge" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	142 <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" value="1" label="Maximum charge" help=""/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	143 <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	144 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	145 <expand macro="adv_opts_macro">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	146 <param argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. "+1" in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	147 <param argument="-scan_regex" type="text" optional="true" value="" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="See documentation for details">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	148 <expand macro="list_string_san" name="scan_regex"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	149 </param>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	150 <param argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same 'mz_file' as used for identification"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	151 <param argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present" help=""/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	152 <param argument="-add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da)" help="This will take quite some time"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	153 <param argument="-concatenate_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit" help=""/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	154 <param argument="-number_of_hits" type="integer" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	156 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	157 <expand macro="list_string_san" name="test"/>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	158 </param>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	159 </expand>
13 250d6a43f66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 11 diff changeset	160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	161 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	162 </param>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	163 </inputs>
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	164 <outputs>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	165 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta">
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	166 <change_format>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	167 <when input="out_type" value="idXML" format="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	168 <when input="out_type" value="mzML" format="mzml"/>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	169 <when input="out_type" value="mzid" format="mzid"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	170 <when input="out_type" value="oms" format="sqlite"/>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	171 <when input="out_type" value="pepXML" format="pepxml"/>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	172 <when input="out_type" value="xquest.xml" format="xquest.xml"/>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	173 </change_format>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	174 </data>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	177 </data>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	178 </outputs>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	179 <tests>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	180 <!-- TOPP_IDFileConverter_1 -->
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	181 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	182 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	183 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	184 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	185 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	186 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	187 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	188 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	189 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	190 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	191 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	192 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	193 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	194 <output name="out" value="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	195 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	196 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	197 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	198 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	199 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	200 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	201 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	202 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	203 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	204 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	205 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	206 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	207 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	208 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	209 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	210 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	211 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	212 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	213 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	214 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	215 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	216 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	217 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	218 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	219 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	220 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	221 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	222 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	223 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	224 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	225 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	226 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	227 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	228 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	229 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	230 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	231 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	232 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	233 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	234 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	235 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	236 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	237 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	238 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	239 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	240 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	241 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	242 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	243 <!-- TOPP_IDFileConverter_2 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	244 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	245 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	246 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	247 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	248 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	249 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	250 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	251 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	252 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	253 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	254 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	255 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	256 <param name="in" value="PepXMLFile_test.pepxml"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	257 <output name="out" value="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	258 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	259 <param name="mz_file" value="PepXMLFile_test.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	260 <param name="mz_name" value="PepXMLFile_test"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	261 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	262 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	263 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	264 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	265 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	266 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	267 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	268 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	269 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	270 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	271 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	272 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	273 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	274 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	275 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	276 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	277 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	278 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	279 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	280 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	281 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	282 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	283 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	284 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	285 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	286 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	287 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	288 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	289 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	290 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	291 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	292 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	293 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	294 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	295 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	297 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	298 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	299 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	300 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	301 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	302 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	303 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	304 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	305 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	306 <!-- TOPP_IDFileConverter_3 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	307 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	308 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	309 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	310 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	311 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	312 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	313 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	314 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	315 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	316 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	317 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	318 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	319 <param name="in" value="IDFileConverter_3_input.protXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	320 <output name="out" value="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	321 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	322 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	323 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	324 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	325 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	326 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	327 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	328 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	329 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	330 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	331 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	332 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	333 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	334 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	335 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	336 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	337 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	338 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	339 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	340 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	341 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	342 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	343 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	344 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	345 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	346 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	347 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	348 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	349 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	350 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	351 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	352 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	353 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	354 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	355 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	356 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	357 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	358 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	359 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	360 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	361 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	362 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	363 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	364 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	365 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	366 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	367 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	368 <!-- TOPP_IDFileConverter_5 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	369 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	370 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	371 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	372 <param name="scan_regex" value="scan=(?<SCAN>\d+)"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	373 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	374 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	375 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	376 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	377 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	378 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	379 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	380 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	381 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	382 <output name="out" value="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	383 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	384 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	385 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	386 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	387 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	388 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	389 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	390 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	391 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	392 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	393 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	394 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	395 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	396 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	397 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	398 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	399 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	400 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	401 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	402 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	403 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	404 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	405 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	406 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	407 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	408 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	409 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	410 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	411 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	412 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	413 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	414 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	415 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	416 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	417 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	418 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	419 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	420 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	421 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	422 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	423 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	424 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	425 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	426 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	427 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	428 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	429 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	430 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	431 <!-- TOPP_IDFileConverter_6 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	432 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	433 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	434 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	435 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	436 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	437 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	438 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	439 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	440 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	441 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	442 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	443 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	444 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	445 <output name="out" value="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	446 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	447 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	448 <param name="mz_name" value="F025589.dat.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	449 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	450 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	451 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	452 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	453 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	454 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	455 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	456 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	457 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	458 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	459 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	460 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	461 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	462 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	463 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	464 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	465 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	466 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	467 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	468 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	469 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	470 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	471 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	472 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	473 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	474 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	475 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	476 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	477 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	478 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	479 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	480 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	481 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	482 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	483 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	484 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	485 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	486 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	487 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	488 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	489 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	490 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	491 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	492 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	493 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	494 <!-- TOPP_IDFileConverter_7 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	495 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	496 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	497 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	498 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	499 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	500 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	501 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	502 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	503 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	504 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	505 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	506 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	507 <param name="in" value="IDFileConverter_7_input1.xml"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	508 <output name="out" value="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	509 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	510 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	511 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	512 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	513 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	514 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	515 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	516 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	517 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	518 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	519 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	520 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	521 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	522 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	523 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	524 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	525 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	526 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	527 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	528 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	529 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	530 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	531 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	532 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	533 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	534 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	535 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	536 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	537 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	538 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	539 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	540 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	541 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	542 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	543 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	544 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	545 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	546 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	547 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	548 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	549 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	550 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	551 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	552 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	553 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	554 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	555 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	556 <!-- TOPP_IDFileConverter_8 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	557 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	558 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	559 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	560 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	561 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	562 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	563 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	564 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	565 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	566 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	567 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	568 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	569 <param name="in" value="IDFileConverter_8_input.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	570 <output name="out" value="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	571 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	572 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	573 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	574 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	575 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	576 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	577 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	578 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	579 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	580 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	581 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	582 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	583 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	584 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	585 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	586 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	587 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	588 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	589 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	590 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	591 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	592 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	593 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	594 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	595 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	596 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	597 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	598 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	599 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	600 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	601 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	602 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	603 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	604 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	605 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	606 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	607 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	608 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	609 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	610 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	611 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	612 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	613 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	614 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	615 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	616 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	617 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	618 <!-- TOPP_IDFileConverter_9 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	619 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	620 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	621 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	622 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	623 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	624 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	625 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	626 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	627 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	628 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	629 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	630 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	631 <param name="in" value="IDFileConverter_9_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	632 <output name="out" value="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	633 <param name="out_type" value="mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	634 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	635 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	636 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	637 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	638 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	639 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	640 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	641 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	642 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	643 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	644 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	645 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	646 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	647 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	648 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	649 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	650 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	651 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	652 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	653 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	654 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	655 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	656 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	657 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	658 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	659 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	660 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	661 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	662 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	663 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	664 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	665 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	666 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	667 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	668 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	669 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	670 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	671 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	672 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	673 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	674 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	675 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	676 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	677 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	678 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	679 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	680 <!-- TOPP_IDFileConverter_10 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	681 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	682 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	683 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	684 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	685 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	686 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	687 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	688 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	689 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	690 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	691 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	692 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	693 <param name="in" value="IDFileConverter_10_input.pepXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	694 <output name="out" value="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	695 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	696 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	697 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	698 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	699 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	700 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	701 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	702 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	703 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	704 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	705 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	706 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	707 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	708 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	709 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	710 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	711 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	712 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	713 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	714 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	715 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	716 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	717 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	718 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	719 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	720 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	721 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	722 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	723 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	724 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	725 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	726 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	727 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	728 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	729 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	730 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	731 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	732 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	733 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	734 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	735 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	736 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	737 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	738 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	739 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	740 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	741 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	742 <!-- TOPP_IDFileConverter_11 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	743 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	744 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	745 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	746 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	747 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	748 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	749 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	750 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	751 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	752 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	753 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	754 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	755 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	756 <output name="out" value="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	757 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	758 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	759 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	760 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	761 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	762 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	763 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	764 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	765 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	766 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	767 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	768 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	769 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	770 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	771 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	772 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	773 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	774 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	775 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	776 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	777 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	778 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	779 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	780 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	781 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	782 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	783 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	784 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	785 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	786 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	787 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	788 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	789 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	790 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	791 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	792 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	793 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	794 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	795 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	796 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	797 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	798 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	799 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	800 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	801 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	802 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	803 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	804 <!-- TOPP_IDFileConverter_12 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	805 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	806 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	807 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	808 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	809 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	810 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	811 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	812 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	813 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	814 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	815 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	816 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	817 <param name="in" value="IDFileConverter_12_input.psms"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	818 <output name="out" value="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	819 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	820 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	821 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	822 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	823 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	824 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	825 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	826 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	827 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	828 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	829 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	830 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	831 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	832 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	833 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	834 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	835 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	836 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	837 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	838 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	839 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	840 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	841 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	842 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	843 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	844 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	845 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	846 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	847 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	848 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	849 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	850 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	851 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	852 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	853 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	854 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	855 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	856 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	857 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	858 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	859 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	860 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	861 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	862 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	863 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	864 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	865 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	866 <!-- TOPP_IDFileConverter_13 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	867 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	868 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	869 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	870 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	871 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	872 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	873 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	874 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	875 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	876 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	877 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	878 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	879 <param name="in" value="IDFileConverter_12_input.psms"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	880 <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	881 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	882 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	883 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	884 <param name="score_type" value="PEP"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	885 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	886 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	887 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	888 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	889 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	890 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	891 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	892 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	893 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	894 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	895 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	896 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	897 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	898 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	899 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	900 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	901 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	902 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	903 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	904 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	905 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	906 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	907 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	908 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	909 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	910 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	911 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	912 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	913 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	914 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	915 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	916 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	917 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	919 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	920 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	921 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	922 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	923 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	924 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	925 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	926 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	927 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	928 <!-- TOPP_IDFileConverter_14 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	929 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	930 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	931 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	932 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	933 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	934 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	935 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	936 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	937 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	938 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	939 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	940 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	941 <param name="in" value="IDFileConverter_12_input.psms"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	942 <output name="out" value="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	943 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	944 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	945 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	946 <param name="score_type" value="score"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	947 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	948 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	949 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	950 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	951 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	952 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	953 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	954 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	955 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	956 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	957 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	958 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	959 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	960 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	961 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	962 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	963 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	964 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	965 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	966 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	967 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	968 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	969 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	970 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	971 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	972 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	973 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	974 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	975 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	976 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	977 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	978 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	979 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	980 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	981 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	982 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	983 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	984 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	985 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	986 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	987 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	988 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	989 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	990 <!-- TOPP_IDFileConverter_15 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	991 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	992 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	993 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	994 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	995 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	996 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	997 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	998 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	999 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1000 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1001 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1002 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1003 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1004 <output name="out" value="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1005 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1006 <param name="mz_file" value="spectra.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1007 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1008 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1009 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1010 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1011 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1012 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1013 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1014 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1015 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1016 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1017 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1018 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1019 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1020 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1021 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1022 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1023 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1024 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1025 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1026 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1027 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1028 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1029 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1030 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1031 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1032 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1033 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1034 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1035 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1036 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1037 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1038 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1039 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1040 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1041 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1042 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1043 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1044 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1045 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1046 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1047 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1048 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1049 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1050 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1051 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1052 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1053 <!-- TOPP_IDFileConverter_16 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1054 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1055 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1056 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1057 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1058 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1059 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1060 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1061 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1062 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1063 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1064 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1065 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1066 <param name="in" value="IDFileConverter_16_input.pepXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1067 <output name="out" value="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1068 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1069 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1070 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1071 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1072 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1073 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1074 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1075 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1076 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1077 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1078 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1079 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1080 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1081 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1082 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1083 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1084 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1085 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1086 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1087 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1088 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1089 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1090 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1091 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1092 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1093 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1094 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1095 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1096 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1097 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1098 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1099 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1100 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1101 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1102 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1103 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1104 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1105 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1106 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1107 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1108 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1109 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1110 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1111 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1112 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1113 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1114 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1115 <!-- TOPP_IDFileConverter_17 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1116 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1117 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1118 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1119 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1120 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1121 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1122 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1123 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1124 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1125 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1126 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1127 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1128 <param name="in" value="IDFileConverter_17_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1129 <output name="out" value="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1130 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1131 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1132 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1133 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1134 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1135 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1136 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1137 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1138 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1139 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1140 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1141 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1142 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1143 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1144 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1145 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1146 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1147 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1148 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1149 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1150 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1151 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1152 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1153 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1154 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1155 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1156 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1157 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1158 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1159 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1160 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1161 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1162 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1163 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1164 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1165 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1166 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1167 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1168 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1169 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1170 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1171 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1172 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1173 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1174 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1175 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1176 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1177 <!-- TOPP_IDFileConverter_18 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1178 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1179 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1180 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1181 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1182 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1183 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1184 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1185 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1186 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1187 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1188 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1189 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1190 <param name="in" value="IDFileConverter_18_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1191 <output name="out" value="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1192 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1193 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1194 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1195 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1196 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1197 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1198 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1199 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1200 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1201 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1202 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1203 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1204 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1205 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1206 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1207 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1208 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1209 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1210 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1211 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1212 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1213 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1214 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1215 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1216 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1217 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1218 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1219 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1220 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1221 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1222 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1223 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1224 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1225 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1226 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1227 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1228 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1230 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1231 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1232 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1233 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1234 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1235 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1236 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1237 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1238 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1239 <!-- TOPP_IDFileConverter_19 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1240 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1241 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1242 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1243 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1244 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1245 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1246 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1247 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1248 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1249 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1250 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1251 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1252 <param name="in" value="IDFileConverter_19_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1253 <output name="out" value="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1254 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1255 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1256 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1257 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1258 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1259 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1260 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1261 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1262 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1263 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1264 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1265 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1266 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1267 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1268 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1269 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1270 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1271 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1272 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1273 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1274 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1275 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1276 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1277 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1278 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1279 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1280 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1281 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1282 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1283 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1284 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1285 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1286 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1287 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1288 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1289 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1290 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1291 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1292 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1293 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1294 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1295 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1296 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1297 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1298 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1299 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1300 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1301 <!-- TOPP_IDFileConverter_20 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1302 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1303 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1304 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1305 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1306 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1307 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1308 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1309 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1310 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1311 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1312 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1313 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1314 <param name="in" value="IDFileConverter_20_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1315 <output name="out" value="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1316 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1317 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1318 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1319 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1320 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1321 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1322 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1323 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1324 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1325 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1326 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1327 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1328 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1329 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1330 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1331 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1332 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1333 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1334 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1335 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1336 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1337 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1338 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1339 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1340 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1341 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1342 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1343 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1344 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1345 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1346 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1347 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1348 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1349 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1350 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1351 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1352 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1354 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1355 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1356 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1357 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1358 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1359 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1360 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1361 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1362 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1363 <!-- TOPP_IDFileConverter_21 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1364 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1365 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1366 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1367 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1368 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1369 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1370 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1371 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1372 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1373 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1374 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1375 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1376 <param name="in" value="IDFileConverter_21_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1377 <output name="out" value="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1378 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1379 <param name="mz_file" value="IDMapper_4_input.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1380 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1381 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1382 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1383 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1384 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1385 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1386 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1387 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1388 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1389 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1390 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1391 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1392 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1393 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1394 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1395 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1396 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1397 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1398 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1399 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1400 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1401 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1402 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1403 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1404 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1405 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1406 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1407 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1408 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1409 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1410 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1411 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1412 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1413 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1414 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1415 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1416 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1417 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1418 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1419 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1420 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1421 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1422 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1423 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1424 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1425 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1426 <!-- TOPP_IDFileConverter_22 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1427 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1428 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1429 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1430 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1431 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1432 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1433 <param name="add_ionmatch_annotation" value="0.01"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1434 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1435 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1436 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1437 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1438 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1439 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1440 <output name="out" value="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1441 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1442 <param name="mz_file" value="spectra.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1443 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1444 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1445 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1446 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1447 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1448 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1449 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1450 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1451 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1452 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1453 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1454 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1455 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1456 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1457 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1458 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1459 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1460 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1461 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1462 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1463 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1464 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1465 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1466 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1467 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1468 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1469 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1470 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1471 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1472 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1473 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1474 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1475 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1476 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1477 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1478 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1479 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1480 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1481 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1482 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1483 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1484 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1485 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1486 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1487 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1488 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1489 <!-- TOPP_IDFileConverter_23 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1490 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1491 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1492 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1493 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1494 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1495 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1496 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1497 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1498 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1499 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1500 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1501 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1502 <param name="in" value="IDFileConverter_23_input.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1503 <output name="out" value="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1504 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1505 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1506 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1507 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1508 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1509 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1510 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1511 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1512 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1513 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1514 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1515 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1516 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1517 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1518 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1519 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1520 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1521 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1522 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1523 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1524 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1525 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1526 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1527 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1528 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1529 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1530 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1531 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1532 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1533 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1534 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1535 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1536 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1537 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1538 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1539 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1540 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1541 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1542 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1543 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1544 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1545 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1546 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1547 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1548 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1549 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1550 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1551 <!-- TOPP_IDFileConverter_24 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1552 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1553 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1554 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1555 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1556 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1557 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1558 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1559 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1560 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1561 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1562 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1563 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1564 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1565 <output name="out" value="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1566 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1567 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1568 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1569 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1570 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1571 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1572 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1573 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1574 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1575 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1576 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1577 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1578 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1579 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1580 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1581 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1582 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1583 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1584 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1585 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1586 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1587 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1588 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1589 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1590 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1591 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1592 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1593 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1594 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1595 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1596 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1597 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1598 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1599 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1600 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1601 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1602 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1603 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1604 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1605 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1606 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1607 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1608 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1609 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1610 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1611 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1612 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1613 <!-- TOPP_IDFileConverter_25 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1614 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1615 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1616 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1617 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1618 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1619 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1620 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1621 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1622 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1623 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1624 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1625 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1626 <param name="in" value="IDFileConverter_25_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1627 <output name="out" value="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1628 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1629 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1630 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1631 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1632 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1633 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1634 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1635 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1636 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1637 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1638 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1639 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1640 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1641 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1642 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1643 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1644 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1645 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1646 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1647 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1648 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1649 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1650 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1651 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1652 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1653 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1654 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1655 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1656 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1657 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1658 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1659 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1660 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1661 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1662 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1663 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1664 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1665 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1666 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1667 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1668 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1669 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1670 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1671 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1672 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1673 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1674 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1675 <!-- TOPP_IDFileConverter_26 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1676 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1677 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1678 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1679 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1680 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1681 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1682 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1683 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1684 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1685 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1686 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1687 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1688 <param name="in" value="IDFileConverter_26_input.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1689 <output name="out" value="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1690 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1691 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1692 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1693 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1694 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1695 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1696 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1697 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1698 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1699 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1700 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1701 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1702 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1703 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1704 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1705 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1706 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1707 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1708 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1709 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1710 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1711 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1712 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1713 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1714 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1715 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1716 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1717 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1718 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1719 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1720 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1721 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1722 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1723 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1724 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1725 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1726 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1728 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1729 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1730 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1731 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1732 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1733 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1734 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1735 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1736 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1737 <!-- TOPP_IDFileConverter_27 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1738 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1739 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1740 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1741 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1742 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1743 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1744 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1745 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1746 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1747 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1748 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1749 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1750 <param name="in" value="IDFileConverter_27_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1751 <output name="out" value="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1752 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1753 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1754 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1755 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1756 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1757 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1758 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1759 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1760 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1761 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1762 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1763 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1764 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1765 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1766 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1767 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1768 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1769 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1770 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1771 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1772 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1773 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1774 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1775 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1776 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1777 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1778 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1779 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1780 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1781 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1782 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1783 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1784 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1785 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1786 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1787 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1788 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1789 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1790 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1791 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1792 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1793 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1794 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1795 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1796 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1797 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1798 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1799 <!-- TOPP_IDFileConverter_28 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1800 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1801 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1802 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1803 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1804 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1805 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1806 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1807 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1808 <param name="number_of_hits" value="-1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1809 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1810 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1811 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1812 <param name="in" value="IDFileConverter_27_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1813 <output name="out" value="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1814 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1815 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1816 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1817 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1818 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1819 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1820 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1821 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1822 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1823 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1824 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1825 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1826 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1827 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1828 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1829 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1830 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1831 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1832 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1833 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1834 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1835 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1836 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1837 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1838 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1839 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1840 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1841 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1842 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1843 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1844 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1845 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1846 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1847 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1848 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1849 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1850 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1851 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1852 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1853 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1854 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1855 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1856 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1857 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1858 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1859 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1860 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1861 <!-- TOPP_IDFileConverter_29 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1862 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1863 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1864 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1865 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1866 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1867 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1868 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1869 <param name="concatenate_peptides" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1870 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1871 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1872 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1873 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1874 <param name="in" value="IDFileConverter_27_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1875 <output name="out" value="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1876 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1877 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1878 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1879 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1880 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1881 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1882 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1883 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1884 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1885 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1886 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1887 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1888 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1889 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1890 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1891 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1892 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1893 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1894 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1895 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1896 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1897 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1898 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1899 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1900 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1901 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1902 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1903 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1904 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1905 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1906 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1907 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1908 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1909 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1910 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1911 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1912 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1913 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1914 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1915 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1916 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1917 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1918 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1919 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1920 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1921 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1922 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1923 <!-- TOPP_IDFileConverter_30 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1924 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1925 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1926 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1927 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1928 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1929 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1930 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1931 <param name="concatenate_peptides" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1932 <param name="number_of_hits" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1933 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1934 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1935 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1936 <param name="in" value="IDFileConverter_27_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1937 <output name="out" value="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1938 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1939 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1940 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1941 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1942 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1943 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1944 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1945 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1946 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1947 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1948 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1949 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1950 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1951 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1952 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1953 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1954 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1955 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1956 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1957 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1958 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1959 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1960 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1961 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1962 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1963 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1964 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1965 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1966 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1967 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1968 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1969 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1970 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1971 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1972 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1973 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1974 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1976 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1977 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1978 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1979 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1980 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1981 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1982 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1983 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1984 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1985 <!-- TOPP_IDFileConverter_31 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1986 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1987 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1988 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1989 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1990 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1991 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1992 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1993 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1994 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1995 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1996 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1997 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	1998 <param name="in" value="IDFileConverter_31_input.mzid"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	1999 <output name="out" value="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2000 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2001 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2002 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2003 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2004 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2005 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2006 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2007 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2008 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2009 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2010 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2011 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2012 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2013 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2014 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2015 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2016 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2017 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2018 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2019 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2020 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2021 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2022 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2023 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2024 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2025 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2026 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2027 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2028 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2029 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2030 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2031 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2032 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2033 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2034 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2035 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2036 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2037 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2038 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2039 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2040 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2041 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2042 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2043 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2044 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2045 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2046 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2047 <!-- TOPP_IDFileConverter_32 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2048 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2049 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2050 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2051 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2052 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2053 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2054 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2055 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2056 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2057 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2058 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2059 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2060 <param name="in" value="IDFileConverter_32_input.FASTA"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2061 <output name="out" value="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2062 <param name="out_type" value="mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2063 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2064 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2065 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2066 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2067 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2068 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2069 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2070 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2071 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2072 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2073 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2074 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2075 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2076 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2077 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2078 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2079 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2080 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2081 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2082 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2083 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2084 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2085 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2086 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2087 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2088 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2089 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2090 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2091 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2092 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2093 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2094 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2095 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2096 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2097 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2098 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2099 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2100 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2101 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2102 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2103 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2104 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2105 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2106 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2107 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2108 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2109 <!-- TOPP_IDFileConverter_33 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2110 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2111 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2112 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2113 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2114 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2115 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2116 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2117 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2118 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2119 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2120 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2121 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2122 <param name="in" value="IDFileConverter_32_input.FASTA"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2123 <output name="out" value="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2124 <param name="out_type" value="mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2125 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2126 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2127 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2128 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2129 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2130 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2131 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2132 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2133 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2134 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2135 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2136 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2137 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2138 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2139 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2140 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2141 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2142 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2143 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2144 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2145 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2146 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2147 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2148 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2149 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2150 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2151 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2152 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2153 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2154 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2155 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2156 <param name="missed_cleavages" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2157 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2158 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2159 <param name="precursor_charge" value="3"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2160 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2161 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2162 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2163 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2164 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2165 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2166 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2167 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2168 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2169 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2170 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2171 <!-- TOPP_IDFileConverter_34_1 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2172 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2173 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2174 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2175 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2176 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2177 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2178 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2179 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2180 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2181 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2182 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2183 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2184 <param name="in" value="IDFileConverter_34_input.idXML"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2185 <output name="out" value="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2186 <param name="out_type" value="oms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2187 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2188 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2189 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2190 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2191 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2192 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2193 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2194 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2195 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2196 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2197 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2198 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2199 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2200 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2201 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2202 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2203 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2204 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2205 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2206 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2207 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2208 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2209 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2210 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2211 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2212 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2213 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2214 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2215 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2216 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2217 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2218 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2219 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2220 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2221 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2222 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2224 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2225 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2226 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2227 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2228 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2229 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2230 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2231 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2232 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2233 <!-- TOPP_IDFileConverter_34_2 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2234 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2235 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2236 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2237 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2238 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2239 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2240 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2241 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2242 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2243 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2244 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2245 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2246 <param name="in" value="IDFileConverter_34_output1.oms"/>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2247 <output name="out" value="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2248 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2249 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2250 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2251 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2252 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2253 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2254 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2255 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2256 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2257 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2258 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2259 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2260 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2261 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2262 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2263 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2264 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2265 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2266 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2267 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2268 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2269 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2270 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2271 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2272 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2273 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2274 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2275 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2276 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2277 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2278 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2279 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2280 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2281 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2282 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2283 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2284 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2285 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2286 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2287 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2288 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2289 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2290 </output>
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2291 <assert_stdout>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2292 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2293 </assert_stdout>
15 7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 13 diff changeset	2294 </test>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	2295 </tests>
43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	2296 <help><![CDATA[Converts identification engine file formats.
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2297
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2298
16 5e9c35b8d194 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 15 diff changeset	2299 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFileConverter.html]]></help>
11 43a1db77b7a6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 9 diff changeset	2300 <expand macro="references"/>
0 bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2301 </tool>

Mercurial > repos > galaxyp > openms_idfileconverter

annotate IDFileConverter.xml @ 16:5e9c35b8d194 draft default tip