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

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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
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15:7d0eb300f360 16:5e9c35b8d194
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converts identification engine file formats.</description> 4 <description>Converts identification engine file formats</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDFileConverter</token> 6 <token name="@EXECUTABLE@">IDFileConverter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $mz_file: 19 #if $mz_file:
21 mkdir mz_file && 20 mkdir mz_file &&
22 ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' && 21 cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
23 #end if 22 #end if
24 23
25 ## Main program call 24 ## Main program call
26 25
27 set -o pipefail && 26 set -o pipefail &&
45 <configfiles> 44 <configfiles>
46 <inputs name="args_json" data_style="paths"/> 45 <inputs name="args_json" data_style="paths"/>
47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
48 </configfiles> 47 </configfiles>
49 <inputs> 48 <inputs>
50 <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" optional="false" 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)"/> 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)"/>
51 <param argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help=""> 50 <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
52 <option value="fasta">fasta</option> 51 <option value="fasta">fasta</option>
53 <option value="idXML">idxml</option> 52 <option value="idXML">idxml</option>
54 <option value="mzML">mzml</option> 53 <option value="mzML">mzml</option>
55 <option value="mzid">mzid</option> 54 <option value="mzid">mzid</option>
56 <option value="oms">sqlite (oms)</option> 55 <option value="oms">sqlite (oms)</option>
57 <option value="pepXML">pepxml</option> 56 <option value="pepXML">pepxml</option>
58 <option value="xquest.xml">xquest.xml</option> 57 <option value="xquest.xml">xquest.xml</option>
58 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
59 <expand macro="list_string_san" name="out_type"/> 59 <expand macro="list_string_san" name="out_type"/>
60 </param> 60 </param>
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)"/> 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)"/>
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'"> 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'">
63 <expand macro="list_string_san" name="mz_name"/> 63 <expand macro="list_string_san" name="mz_name"/>
64 </param> 64 </param>
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"/> 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"/>
66 <param argument="-score_type" type="select" optional="true" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help=""> 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="">
67 <option value="qvalue" selected="true">qvalue</option> 67 <option value="qvalue" selected="true">qvalue</option>
68 <option value="PEP">PEP</option> 68 <option value="PEP">PEP</option>
69 <option value="score">score</option> 69 <option value="score">score</option>
70 <expand macro="list_string_san" name="score_type"/> 70 <expand macro="list_string_san" name="score_type"/>
71 </param> 71 </param>
72 <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false"> 72 <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
73 <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" optional="true" 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"> 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">
74 <option value="none" selected="true">none</option> 74 <option value="none" selected="true">none</option>
75 <option value="coarse">coarse</option> 75 <option value="coarse">coarse</option>
76 <option value="fine">fine</option> 76 <option value="fine">fine</option>
77 <expand macro="list_string_san" name="isotope_model"/> 77 <expand macro="list_string_san" name="isotope_model"/>
78 </param> 78 </param>
79 <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/> 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=""/>
80 <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
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=""/> 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=""/>
94 <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/> 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=""/>
95 <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/> 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=""/>
96 <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/> 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=""/>
97 <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/> 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=""/>
98 <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/> 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=""/>
99 <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/> 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=""/>
100 <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/> 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=""/>
101 <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/> 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=""/>
102 <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/> 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=""/>
103 <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/> 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=""/>
104 <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" optional="true" label="Enzym used to digest the fasta proteins" help=""> 104 <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" label="Enzym used to digest the fasta proteins" help="">
105 <option value="Trypsin" selected="true">Trypsin</option> 105 <option value="Trypsin" selected="true">Trypsin</option>
106 <option value="Arg-C">Arg-C</option>
107 <option value="no cleavage">no cleavage</option>
108 <option value="unspecific cleavage">unspecific cleavage</option>
109 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
110 <option value="Glu-C+P">Glu-C+P</option>
111 <option value="PepsinA + P">PepsinA + P</option>
112 <option value="cyanogen-bromide">cyanogen-bromide</option>
113 <option value="Clostripain/P">Clostripain/P</option>
114 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
115 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
116 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
117 <option value="2-iodobenzoate">2-iodobenzoate</option>
118 <option value="iodosobenzoate">iodosobenzoate</option>
119 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
120 <option value="Trypsin/P">Trypsin/P</option>
121 <option value="V8-DE">V8-DE</option>
122 <option value="Arg-C/P">Arg-C/P</option>
123 <option value="Asp-N">Asp-N</option>
124 <option value="Asp-N/B">Asp-N/B</option>
125 <option value="Asp-N_ambic">Asp-N_ambic</option>
106 <option value="Chymotrypsin">Chymotrypsin</option> 126 <option value="Chymotrypsin">Chymotrypsin</option>
107 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 127 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
108 <option value="CNBr">CNBr</option> 128 <option value="CNBr">CNBr</option>
109 <option value="Formic_acid">Formic_acid</option> 129 <option value="Formic_acid">Formic_acid</option>
110 <option value="leukocyte elastase">leukocyte elastase</option>
111 <option value="proline endopeptidase">proline endopeptidase</option>
112 <option value="Arg-C/P">Arg-C/P</option>
113 <option value="Asp-N">Asp-N</option>
114 <option value="Asp-N/B">Asp-N/B</option>
115 <option value="Asp-N_ambic">Asp-N_ambic</option>
116 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
117 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
118 <option value="2-iodobenzoate">2-iodobenzoate</option>
119 <option value="iodosobenzoate">iodosobenzoate</option>
120 <option value="cyanogen-bromide">cyanogen-bromide</option>
121 <option value="Clostripain/P">Clostripain/P</option>
122 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
123 <option value="no cleavage">no cleavage</option>
124 <option value="unspecific cleavage">unspecific cleavage</option>
125 <option value="Lys-C">Lys-C</option> 130 <option value="Lys-C">Lys-C</option>
126 <option value="Lys-N">Lys-N</option> 131 <option value="Lys-N">Lys-N</option>
127 <option value="Lys-C/P">Lys-C/P</option> 132 <option value="Lys-C/P">Lys-C/P</option>
128 <option value="PepsinA">PepsinA</option> 133 <option value="PepsinA">PepsinA</option>
129 <option value="TrypChymo">TrypChymo</option> 134 <option value="TrypChymo">TrypChymo</option>
130 <option value="Trypsin/P">Trypsin/P</option>
131 <option value="V8-DE">V8-DE</option>
132 <option value="V8-E">V8-E</option> 135 <option value="V8-E">V8-E</option>
133 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 136 <option value="leukocyte elastase">leukocyte elastase</option>
134 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 137 <option value="proline endopeptidase">proline endopeptidase</option>
135 <option value="Glu-C+P">Glu-C+P</option>
136 <option value="PepsinA + P">PepsinA + P</option>
137 <option value="Arg-C">Arg-C</option>
138 <expand macro="list_string_san" name="enzyme"/> 138 <expand macro="list_string_san" name="enzyme"/>
139 </param> 139 </param>
140 <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" optional="true" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/> 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=""/>
141 <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" optional="true" value="1" label="Minimum charge" help=""/> 141 <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" value="1" label="Minimum charge" help=""/>
142 <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" optional="true" value="1" label="Maximum charge" help=""/> 142 <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" value="1" label="Maximum charge" help=""/>
143 <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" optional="true" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/> 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)"/>
144 </section> 144 </section>
145 <expand macro="adv_opts_macro"> 145 <expand macro="adv_opts_macro">
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. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/> 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. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
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"> 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">
148 <expand macro="list_string_san" name="scan_regex"/> 148 <expand macro="list_string_san" name="scan_regex"/>
149 </param> 149 </param>
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"/> 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"/>
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=""/> 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=""/>
152 <param argument="-add_ionmatch_annotation" type="float" optional="true" 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"/> 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"/>
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=""/> 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=""/>
154 <param argument="-number_of_hits" type="integer" optional="true" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/> 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"/>
155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 156 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
157 <expand macro="list_string_san" name="test"/> 157 <expand macro="list_string_san" name="test"/>
158 </param> 158 </param>
159 </expand> 159 </expand>
160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
161 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 161 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
174 </data> 174 </data>
175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
177 </data> 177 </data>
178 </outputs> 178 </outputs>
179 <tests><!-- TOPP_IDFileConverter_1 --> 179 <tests>
180 <!-- TOPP_IDFileConverter_1 -->
180 <test expect_num_outputs="2"> 181 <test expect_num_outputs="2">
181 <section name="adv_opts"> 182 <section name="adv_opts">
182 <param name="ignore_proteins_per_peptide" value="false"/> 183 <param name="ignore_proteins_per_peptide" value="false"/>
183 <param name="scan_regex" value=""/> 184 <param name="scan_regex" value=""/>
184 <param name="no_spectra_data_override" value="false"/> 185 <param name="no_spectra_data_override" value="false"/>
188 <param name="number_of_hits" value="1"/> 189 <param name="number_of_hits" value="1"/>
189 <param name="force" value="false"/> 190 <param name="force" value="false"/>
190 <param name="test" value="true"/> 191 <param name="test" value="true"/>
191 </section> 192 </section>
192 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> 193 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
193 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 194 <output name="out" value="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
194 <param name="out_type" value="idXML"/> 195 <param name="out_type" value="idXML"/>
195 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> 196 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
196 <param name="mz_name" value=""/> 197 <param name="mz_name" value=""/>
197 <param name="peptideprophet_analyzed" value="false"/> 198 <param name="peptideprophet_analyzed" value="false"/>
198 <param name="score_type" value="qvalue"/> 199 <param name="score_type" value="qvalue"/>
233 <output name="ctd_out" ftype="xml"> 234 <output name="ctd_out" ftype="xml">
234 <assert_contents> 235 <assert_contents>
235 <is_valid_xml/> 236 <is_valid_xml/>
236 </assert_contents> 237 </assert_contents>
237 </output> 238 </output>
239 <assert_stdout>
240 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
241 </assert_stdout>
238 </test> 242 </test>
239 <!-- TOPP_IDFileConverter_2 --> 243 <!-- TOPP_IDFileConverter_2 -->
240 <test expect_num_outputs="2"> 244 <test expect_num_outputs="2">
241 <section name="adv_opts"> 245 <section name="adv_opts">
242 <param name="ignore_proteins_per_peptide" value="false"/> 246 <param name="ignore_proteins_per_peptide" value="false"/>
248 <param name="number_of_hits" value="1"/> 252 <param name="number_of_hits" value="1"/>
249 <param name="force" value="false"/> 253 <param name="force" value="false"/>
250 <param name="test" value="true"/> 254 <param name="test" value="true"/>
251 </section> 255 </section>
252 <param name="in" value="PepXMLFile_test.pepxml"/> 256 <param name="in" value="PepXMLFile_test.pepxml"/>
253 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 257 <output name="out" value="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
254 <param name="out_type" value="idXML"/> 258 <param name="out_type" value="idXML"/>
255 <param name="mz_file" value="PepXMLFile_test.mzML"/> 259 <param name="mz_file" value="PepXMLFile_test.mzML"/>
256 <param name="mz_name" value="PepXMLFile_test"/> 260 <param name="mz_name" value="PepXMLFile_test"/>
257 <param name="peptideprophet_analyzed" value="false"/> 261 <param name="peptideprophet_analyzed" value="false"/>
258 <param name="score_type" value="qvalue"/> 262 <param name="score_type" value="qvalue"/>
293 <output name="ctd_out" ftype="xml"> 297 <output name="ctd_out" ftype="xml">
294 <assert_contents> 298 <assert_contents>
295 <is_valid_xml/> 299 <is_valid_xml/>
296 </assert_contents> 300 </assert_contents>
297 </output> 301 </output>
302 <assert_stdout>
303 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
304 </assert_stdout>
298 </test> 305 </test>
299 <!-- TOPP_IDFileConverter_3 --> 306 <!-- TOPP_IDFileConverter_3 -->
300 <test expect_num_outputs="2"> 307 <test expect_num_outputs="2">
301 <section name="adv_opts"> 308 <section name="adv_opts">
302 <param name="ignore_proteins_per_peptide" value="false"/> 309 <param name="ignore_proteins_per_peptide" value="false"/>
308 <param name="number_of_hits" value="1"/> 315 <param name="number_of_hits" value="1"/>
309 <param name="force" value="false"/> 316 <param name="force" value="false"/>
310 <param name="test" value="true"/> 317 <param name="test" value="true"/>
311 </section> 318 </section>
312 <param name="in" value="IDFileConverter_3_input.protXML"/> 319 <param name="in" value="IDFileConverter_3_input.protXML"/>
313 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 320 <output name="out" value="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
314 <param name="out_type" value="idXML"/> 321 <param name="out_type" value="idXML"/>
315 <param name="mz_name" value=""/> 322 <param name="mz_name" value=""/>
316 <param name="peptideprophet_analyzed" value="false"/> 323 <param name="peptideprophet_analyzed" value="false"/>
317 <param name="score_type" value="qvalue"/> 324 <param name="score_type" value="qvalue"/>
318 <section name="fasta_to_mzml"> 325 <section name="fasta_to_mzml">
352 <output name="ctd_out" ftype="xml"> 359 <output name="ctd_out" ftype="xml">
353 <assert_contents> 360 <assert_contents>
354 <is_valid_xml/> 361 <is_valid_xml/>
355 </assert_contents> 362 </assert_contents>
356 </output> 363 </output>
364 <assert_stdout>
365 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
366 </assert_stdout>
357 </test> 367 </test>
358 <!-- TOPP_IDFileConverter_5 --> 368 <!-- TOPP_IDFileConverter_5 -->
359 <test expect_num_outputs="2"> 369 <test expect_num_outputs="2">
360 <section name="adv_opts"> 370 <section name="adv_opts">
361 <param name="ignore_proteins_per_peptide" value="false"/> 371 <param name="ignore_proteins_per_peptide" value="false"/>
367 <param name="number_of_hits" value="1"/> 377 <param name="number_of_hits" value="1"/>
368 <param name="force" value="false"/> 378 <param name="force" value="false"/>
369 <param name="test" value="true"/> 379 <param name="test" value="true"/>
370 </section> 380 </section>
371 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> 381 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
372 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 382 <output name="out" value="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
373 <param name="out_type" value="idXML"/> 383 <param name="out_type" value="idXML"/>
374 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> 384 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
375 <param name="mz_name" value=""/> 385 <param name="mz_name" value=""/>
376 <param name="peptideprophet_analyzed" value="false"/> 386 <param name="peptideprophet_analyzed" value="false"/>
377 <param name="score_type" value="qvalue"/> 387 <param name="score_type" value="qvalue"/>
412 <output name="ctd_out" ftype="xml"> 422 <output name="ctd_out" ftype="xml">
413 <assert_contents> 423 <assert_contents>
414 <is_valid_xml/> 424 <is_valid_xml/>
415 </assert_contents> 425 </assert_contents>
416 </output> 426 </output>
427 <assert_stdout>
428 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
429 </assert_stdout>
417 </test> 430 </test>
418 <!-- TOPP_IDFileConverter_6 --> 431 <!-- TOPP_IDFileConverter_6 -->
419 <test expect_num_outputs="2"> 432 <test expect_num_outputs="2">
420 <section name="adv_opts"> 433 <section name="adv_opts">
421 <param name="ignore_proteins_per_peptide" value="false"/> 434 <param name="ignore_proteins_per_peptide" value="false"/>
427 <param name="number_of_hits" value="1"/> 440 <param name="number_of_hits" value="1"/>
428 <param name="force" value="false"/> 441 <param name="force" value="false"/>
429 <param name="test" value="true"/> 442 <param name="test" value="true"/>
430 </section> 443 </section>
431 <param name="in" value="IDFileConverter_6_input1.pepXML"/> 444 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
432 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 445 <output name="out" value="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
433 <param name="out_type" value="idXML"/> 446 <param name="out_type" value="idXML"/>
434 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> 447 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
435 <param name="mz_name" value="F025589.dat.mzML"/> 448 <param name="mz_name" value="F025589.dat.mzML"/>
436 <param name="peptideprophet_analyzed" value="false"/> 449 <param name="peptideprophet_analyzed" value="false"/>
437 <param name="score_type" value="qvalue"/> 450 <param name="score_type" value="qvalue"/>
472 <output name="ctd_out" ftype="xml"> 485 <output name="ctd_out" ftype="xml">
473 <assert_contents> 486 <assert_contents>
474 <is_valid_xml/> 487 <is_valid_xml/>
475 </assert_contents> 488 </assert_contents>
476 </output> 489 </output>
490 <assert_stdout>
491 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
492 </assert_stdout>
477 </test> 493 </test>
478 <!-- TOPP_IDFileConverter_7 --> 494 <!-- TOPP_IDFileConverter_7 -->
479 <test expect_num_outputs="2"> 495 <test expect_num_outputs="2">
480 <section name="adv_opts"> 496 <section name="adv_opts">
481 <param name="ignore_proteins_per_peptide" value="false"/> 497 <param name="ignore_proteins_per_peptide" value="false"/>
487 <param name="number_of_hits" value="1"/> 503 <param name="number_of_hits" value="1"/>
488 <param name="force" value="false"/> 504 <param name="force" value="false"/>
489 <param name="test" value="true"/> 505 <param name="test" value="true"/>
490 </section> 506 </section>
491 <param name="in" value="IDFileConverter_7_input1.xml"/> 507 <param name="in" value="IDFileConverter_7_input1.xml"/>
492 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 508 <output name="out" value="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
493 <param name="out_type" value="idXML"/> 509 <param name="out_type" value="idXML"/>
494 <param name="mz_name" value=""/> 510 <param name="mz_name" value=""/>
495 <param name="peptideprophet_analyzed" value="false"/> 511 <param name="peptideprophet_analyzed" value="false"/>
496 <param name="score_type" value="qvalue"/> 512 <param name="score_type" value="qvalue"/>
497 <section name="fasta_to_mzml"> 513 <section name="fasta_to_mzml">
531 <output name="ctd_out" ftype="xml"> 547 <output name="ctd_out" ftype="xml">
532 <assert_contents> 548 <assert_contents>
533 <is_valid_xml/> 549 <is_valid_xml/>
534 </assert_contents> 550 </assert_contents>
535 </output> 551 </output>
552 <assert_stdout>
553 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
554 </assert_stdout>
536 </test> 555 </test>
537 <!-- TOPP_IDFileConverter_8 --> 556 <!-- TOPP_IDFileConverter_8 -->
538 <test expect_num_outputs="2"> 557 <test expect_num_outputs="2">
539 <section name="adv_opts"> 558 <section name="adv_opts">
540 <param name="ignore_proteins_per_peptide" value="false"/> 559 <param name="ignore_proteins_per_peptide" value="false"/>
546 <param name="number_of_hits" value="1"/> 565 <param name="number_of_hits" value="1"/>
547 <param name="force" value="false"/> 566 <param name="force" value="false"/>
548 <param name="test" value="true"/> 567 <param name="test" value="true"/>
549 </section> 568 </section>
550 <param name="in" value="IDFileConverter_8_input.mzid"/> 569 <param name="in" value="IDFileConverter_8_input.mzid"/>
551 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 570 <output name="out" value="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
552 <param name="out_type" value="idXML"/> 571 <param name="out_type" value="idXML"/>
553 <param name="mz_name" value=""/> 572 <param name="mz_name" value=""/>
554 <param name="peptideprophet_analyzed" value="false"/> 573 <param name="peptideprophet_analyzed" value="false"/>
555 <param name="score_type" value="qvalue"/> 574 <param name="score_type" value="qvalue"/>
556 <section name="fasta_to_mzml"> 575 <section name="fasta_to_mzml">
590 <output name="ctd_out" ftype="xml"> 609 <output name="ctd_out" ftype="xml">
591 <assert_contents> 610 <assert_contents>
592 <is_valid_xml/> 611 <is_valid_xml/>
593 </assert_contents> 612 </assert_contents>
594 </output> 613 </output>
614 <assert_stdout>
615 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
616 </assert_stdout>
595 </test> 617 </test>
596 <!-- TOPP_IDFileConverter_9 --> 618 <!-- TOPP_IDFileConverter_9 -->
597 <test expect_num_outputs="2"> 619 <test expect_num_outputs="2">
598 <section name="adv_opts"> 620 <section name="adv_opts">
599 <param name="ignore_proteins_per_peptide" value="false"/> 621 <param name="ignore_proteins_per_peptide" value="false"/>
605 <param name="number_of_hits" value="1"/> 627 <param name="number_of_hits" value="1"/>
606 <param name="force" value="false"/> 628 <param name="force" value="false"/>
607 <param name="test" value="true"/> 629 <param name="test" value="true"/>
608 </section> 630 </section>
609 <param name="in" value="IDFileConverter_9_input.idXML"/> 631 <param name="in" value="IDFileConverter_9_input.idXML"/>
610 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/> 632 <output name="out" value="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
611 <param name="out_type" value="mzid"/> 633 <param name="out_type" value="mzid"/>
612 <param name="mz_name" value=""/> 634 <param name="mz_name" value=""/>
613 <param name="peptideprophet_analyzed" value="false"/> 635 <param name="peptideprophet_analyzed" value="false"/>
614 <param name="score_type" value="qvalue"/> 636 <param name="score_type" value="qvalue"/>
615 <section name="fasta_to_mzml"> 637 <section name="fasta_to_mzml">
649 <output name="ctd_out" ftype="xml"> 671 <output name="ctd_out" ftype="xml">
650 <assert_contents> 672 <assert_contents>
651 <is_valid_xml/> 673 <is_valid_xml/>
652 </assert_contents> 674 </assert_contents>
653 </output> 675 </output>
676 <assert_stdout>
677 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
678 </assert_stdout>
654 </test> 679 </test>
655 <!-- TOPP_IDFileConverter_10 --> 680 <!-- TOPP_IDFileConverter_10 -->
656 <test expect_num_outputs="2"> 681 <test expect_num_outputs="2">
657 <section name="adv_opts"> 682 <section name="adv_opts">
658 <param name="ignore_proteins_per_peptide" value="false"/> 683 <param name="ignore_proteins_per_peptide" value="false"/>
664 <param name="number_of_hits" value="1"/> 689 <param name="number_of_hits" value="1"/>
665 <param name="force" value="false"/> 690 <param name="force" value="false"/>
666 <param name="test" value="true"/> 691 <param name="test" value="true"/>
667 </section> 692 </section>
668 <param name="in" value="IDFileConverter_10_input.pepXML"/> 693 <param name="in" value="IDFileConverter_10_input.pepXML"/>
669 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 694 <output name="out" value="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
670 <param name="out_type" value="idXML"/> 695 <param name="out_type" value="idXML"/>
671 <param name="mz_name" value=""/> 696 <param name="mz_name" value=""/>
672 <param name="peptideprophet_analyzed" value="false"/> 697 <param name="peptideprophet_analyzed" value="false"/>
673 <param name="score_type" value="qvalue"/> 698 <param name="score_type" value="qvalue"/>
674 <section name="fasta_to_mzml"> 699 <section name="fasta_to_mzml">
708 <output name="ctd_out" ftype="xml"> 733 <output name="ctd_out" ftype="xml">
709 <assert_contents> 734 <assert_contents>
710 <is_valid_xml/> 735 <is_valid_xml/>
711 </assert_contents> 736 </assert_contents>
712 </output> 737 </output>
738 <assert_stdout>
739 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
740 </assert_stdout>
713 </test> 741 </test>
714 <!-- TOPP_IDFileConverter_11 --> 742 <!-- TOPP_IDFileConverter_11 -->
715 <test expect_num_outputs="2"> 743 <test expect_num_outputs="2">
716 <section name="adv_opts"> 744 <section name="adv_opts">
717 <param name="ignore_proteins_per_peptide" value="false"/> 745 <param name="ignore_proteins_per_peptide" value="false"/>
723 <param name="number_of_hits" value="1"/> 751 <param name="number_of_hits" value="1"/>
724 <param name="force" value="false"/> 752 <param name="force" value="false"/>
725 <param name="test" value="true"/> 753 <param name="test" value="true"/>
726 </section> 754 </section>
727 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> 755 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
728 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 756 <output name="out" value="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
729 <param name="out_type" value="idXML"/> 757 <param name="out_type" value="idXML"/>
730 <param name="mz_name" value=""/> 758 <param name="mz_name" value=""/>
731 <param name="peptideprophet_analyzed" value="false"/> 759 <param name="peptideprophet_analyzed" value="false"/>
732 <param name="score_type" value="qvalue"/> 760 <param name="score_type" value="qvalue"/>
733 <section name="fasta_to_mzml"> 761 <section name="fasta_to_mzml">
767 <output name="ctd_out" ftype="xml"> 795 <output name="ctd_out" ftype="xml">
768 <assert_contents> 796 <assert_contents>
769 <is_valid_xml/> 797 <is_valid_xml/>
770 </assert_contents> 798 </assert_contents>
771 </output> 799 </output>
800 <assert_stdout>
801 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
802 </assert_stdout>
772 </test> 803 </test>
773 <!-- TOPP_IDFileConverter_12 --> 804 <!-- TOPP_IDFileConverter_12 -->
774 <test expect_num_outputs="2"> 805 <test expect_num_outputs="2">
775 <section name="adv_opts"> 806 <section name="adv_opts">
776 <param name="ignore_proteins_per_peptide" value="false"/> 807 <param name="ignore_proteins_per_peptide" value="false"/>
782 <param name="number_of_hits" value="1"/> 813 <param name="number_of_hits" value="1"/>
783 <param name="force" value="false"/> 814 <param name="force" value="false"/>
784 <param name="test" value="true"/> 815 <param name="test" value="true"/>
785 </section> 816 </section>
786 <param name="in" value="IDFileConverter_12_input.psms"/> 817 <param name="in" value="IDFileConverter_12_input.psms"/>
787 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 818 <output name="out" value="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
788 <param name="out_type" value="idXML"/> 819 <param name="out_type" value="idXML"/>
789 <param name="mz_name" value=""/> 820 <param name="mz_name" value=""/>
790 <param name="peptideprophet_analyzed" value="false"/> 821 <param name="peptideprophet_analyzed" value="false"/>
791 <param name="score_type" value="qvalue"/> 822 <param name="score_type" value="qvalue"/>
792 <section name="fasta_to_mzml"> 823 <section name="fasta_to_mzml">
826 <output name="ctd_out" ftype="xml"> 857 <output name="ctd_out" ftype="xml">
827 <assert_contents> 858 <assert_contents>
828 <is_valid_xml/> 859 <is_valid_xml/>
829 </assert_contents> 860 </assert_contents>
830 </output> 861 </output>
862 <assert_stdout>
863 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
864 </assert_stdout>
831 </test> 865 </test>
832 <!-- TOPP_IDFileConverter_13 --> 866 <!-- TOPP_IDFileConverter_13 -->
833 <test expect_num_outputs="2"> 867 <test expect_num_outputs="2">
834 <section name="adv_opts"> 868 <section name="adv_opts">
835 <param name="ignore_proteins_per_peptide" value="false"/> 869 <param name="ignore_proteins_per_peptide" value="false"/>
841 <param name="number_of_hits" value="1"/> 875 <param name="number_of_hits" value="1"/>
842 <param name="force" value="false"/> 876 <param name="force" value="false"/>
843 <param name="test" value="true"/> 877 <param name="test" value="true"/>
844 </section> 878 </section>
845 <param name="in" value="IDFileConverter_12_input.psms"/> 879 <param name="in" value="IDFileConverter_12_input.psms"/>
846 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 880 <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
847 <param name="out_type" value="idXML"/> 881 <param name="out_type" value="idXML"/>
848 <param name="mz_name" value=""/> 882 <param name="mz_name" value=""/>
849 <param name="peptideprophet_analyzed" value="false"/> 883 <param name="peptideprophet_analyzed" value="false"/>
850 <param name="score_type" value="PEP"/> 884 <param name="score_type" value="PEP"/>
851 <section name="fasta_to_mzml"> 885 <section name="fasta_to_mzml">
885 <output name="ctd_out" ftype="xml"> 919 <output name="ctd_out" ftype="xml">
886 <assert_contents> 920 <assert_contents>
887 <is_valid_xml/> 921 <is_valid_xml/>
888 </assert_contents> 922 </assert_contents>
889 </output> 923 </output>
924 <assert_stdout>
925 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
926 </assert_stdout>
890 </test> 927 </test>
891 <!-- TOPP_IDFileConverter_14 --> 928 <!-- TOPP_IDFileConverter_14 -->
892 <test expect_num_outputs="2"> 929 <test expect_num_outputs="2">
893 <section name="adv_opts"> 930 <section name="adv_opts">
894 <param name="ignore_proteins_per_peptide" value="false"/> 931 <param name="ignore_proteins_per_peptide" value="false"/>
900 <param name="number_of_hits" value="1"/> 937 <param name="number_of_hits" value="1"/>
901 <param name="force" value="false"/> 938 <param name="force" value="false"/>
902 <param name="test" value="true"/> 939 <param name="test" value="true"/>
903 </section> 940 </section>
904 <param name="in" value="IDFileConverter_12_input.psms"/> 941 <param name="in" value="IDFileConverter_12_input.psms"/>
905 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 942 <output name="out" value="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
906 <param name="out_type" value="idXML"/> 943 <param name="out_type" value="idXML"/>
907 <param name="mz_name" value=""/> 944 <param name="mz_name" value=""/>
908 <param name="peptideprophet_analyzed" value="false"/> 945 <param name="peptideprophet_analyzed" value="false"/>
909 <param name="score_type" value="score"/> 946 <param name="score_type" value="score"/>
910 <section name="fasta_to_mzml"> 947 <section name="fasta_to_mzml">
944 <output name="ctd_out" ftype="xml"> 981 <output name="ctd_out" ftype="xml">
945 <assert_contents> 982 <assert_contents>
946 <is_valid_xml/> 983 <is_valid_xml/>
947 </assert_contents> 984 </assert_contents>
948 </output> 985 </output>
986 <assert_stdout>
987 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
988 </assert_stdout>
949 </test> 989 </test>
950 <!-- TOPP_IDFileConverter_15 --> 990 <!-- TOPP_IDFileConverter_15 -->
951 <test expect_num_outputs="2"> 991 <test expect_num_outputs="2">
952 <section name="adv_opts"> 992 <section name="adv_opts">
953 <param name="ignore_proteins_per_peptide" value="false"/> 993 <param name="ignore_proteins_per_peptide" value="false"/>
959 <param name="number_of_hits" value="1"/> 999 <param name="number_of_hits" value="1"/>
960 <param name="force" value="false"/> 1000 <param name="force" value="false"/>
961 <param name="test" value="true"/> 1001 <param name="test" value="true"/>
962 </section> 1002 </section>
963 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> 1003 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
964 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1004 <output name="out" value="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
965 <param name="out_type" value="idXML"/> 1005 <param name="out_type" value="idXML"/>
966 <param name="mz_file" value="spectra.mzML"/> 1006 <param name="mz_file" value="spectra.mzML"/>
967 <param name="mz_name" value=""/> 1007 <param name="mz_name" value=""/>
968 <param name="peptideprophet_analyzed" value="false"/> 1008 <param name="peptideprophet_analyzed" value="false"/>
969 <param name="score_type" value="qvalue"/> 1009 <param name="score_type" value="qvalue"/>
1004 <output name="ctd_out" ftype="xml"> 1044 <output name="ctd_out" ftype="xml">
1005 <assert_contents> 1045 <assert_contents>
1006 <is_valid_xml/> 1046 <is_valid_xml/>
1007 </assert_contents> 1047 </assert_contents>
1008 </output> 1048 </output>
1049 <assert_stdout>
1050 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1051 </assert_stdout>
1009 </test> 1052 </test>
1010 <!-- TOPP_IDFileConverter_16 --> 1053 <!-- TOPP_IDFileConverter_16 -->
1011 <test expect_num_outputs="2"> 1054 <test expect_num_outputs="2">
1012 <section name="adv_opts"> 1055 <section name="adv_opts">
1013 <param name="ignore_proteins_per_peptide" value="false"/> 1056 <param name="ignore_proteins_per_peptide" value="false"/>
1019 <param name="number_of_hits" value="1"/> 1062 <param name="number_of_hits" value="1"/>
1020 <param name="force" value="false"/> 1063 <param name="force" value="false"/>
1021 <param name="test" value="true"/> 1064 <param name="test" value="true"/>
1022 </section> 1065 </section>
1023 <param name="in" value="IDFileConverter_16_input.pepXML"/> 1066 <param name="in" value="IDFileConverter_16_input.pepXML"/>
1024 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1067 <output name="out" value="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1025 <param name="out_type" value="idXML"/> 1068 <param name="out_type" value="idXML"/>
1026 <param name="mz_name" value=""/> 1069 <param name="mz_name" value=""/>
1027 <param name="peptideprophet_analyzed" value="false"/> 1070 <param name="peptideprophet_analyzed" value="false"/>
1028 <param name="score_type" value="qvalue"/> 1071 <param name="score_type" value="qvalue"/>
1029 <section name="fasta_to_mzml"> 1072 <section name="fasta_to_mzml">
1063 <output name="ctd_out" ftype="xml"> 1106 <output name="ctd_out" ftype="xml">
1064 <assert_contents> 1107 <assert_contents>
1065 <is_valid_xml/> 1108 <is_valid_xml/>
1066 </assert_contents> 1109 </assert_contents>
1067 </output> 1110 </output>
1111 <assert_stdout>
1112 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1113 </assert_stdout>
1068 </test> 1114 </test>
1069 <!-- TOPP_IDFileConverter_17 --> 1115 <!-- TOPP_IDFileConverter_17 -->
1070 <test expect_num_outputs="2"> 1116 <test expect_num_outputs="2">
1071 <section name="adv_opts"> 1117 <section name="adv_opts">
1072 <param name="ignore_proteins_per_peptide" value="false"/> 1118 <param name="ignore_proteins_per_peptide" value="false"/>
1078 <param name="number_of_hits" value="1"/> 1124 <param name="number_of_hits" value="1"/>
1079 <param name="force" value="false"/> 1125 <param name="force" value="false"/>
1080 <param name="test" value="true"/> 1126 <param name="test" value="true"/>
1081 </section> 1127 </section>
1082 <param name="in" value="IDFileConverter_17_input.idXML"/> 1128 <param name="in" value="IDFileConverter_17_input.idXML"/>
1083 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> 1129 <output name="out" value="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
1084 <param name="out_type" value="pepXML"/> 1130 <param name="out_type" value="pepXML"/>
1085 <param name="mz_name" value=""/> 1131 <param name="mz_name" value=""/>
1086 <param name="peptideprophet_analyzed" value="false"/> 1132 <param name="peptideprophet_analyzed" value="false"/>
1087 <param name="score_type" value="qvalue"/> 1133 <param name="score_type" value="qvalue"/>
1088 <section name="fasta_to_mzml"> 1134 <section name="fasta_to_mzml">
1122 <output name="ctd_out" ftype="xml"> 1168 <output name="ctd_out" ftype="xml">
1123 <assert_contents> 1169 <assert_contents>
1124 <is_valid_xml/> 1170 <is_valid_xml/>
1125 </assert_contents> 1171 </assert_contents>
1126 </output> 1172 </output>
1173 <assert_stdout>
1174 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1175 </assert_stdout>
1127 </test> 1176 </test>
1128 <!-- TOPP_IDFileConverter_18 --> 1177 <!-- TOPP_IDFileConverter_18 -->
1129 <test expect_num_outputs="2"> 1178 <test expect_num_outputs="2">
1130 <section name="adv_opts"> 1179 <section name="adv_opts">
1131 <param name="ignore_proteins_per_peptide" value="false"/> 1180 <param name="ignore_proteins_per_peptide" value="false"/>
1137 <param name="number_of_hits" value="1"/> 1186 <param name="number_of_hits" value="1"/>
1138 <param name="force" value="false"/> 1187 <param name="force" value="false"/>
1139 <param name="test" value="true"/> 1188 <param name="test" value="true"/>
1140 </section> 1189 </section>
1141 <param name="in" value="IDFileConverter_18_input.idXML"/> 1190 <param name="in" value="IDFileConverter_18_input.idXML"/>
1142 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> 1191 <output name="out" value="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
1143 <param name="out_type" value="pepXML"/> 1192 <param name="out_type" value="pepXML"/>
1144 <param name="mz_name" value=""/> 1193 <param name="mz_name" value=""/>
1145 <param name="peptideprophet_analyzed" value="false"/> 1194 <param name="peptideprophet_analyzed" value="false"/>
1146 <param name="score_type" value="qvalue"/> 1195 <param name="score_type" value="qvalue"/>
1147 <section name="fasta_to_mzml"> 1196 <section name="fasta_to_mzml">
1181 <output name="ctd_out" ftype="xml"> 1230 <output name="ctd_out" ftype="xml">
1182 <assert_contents> 1231 <assert_contents>
1183 <is_valid_xml/> 1232 <is_valid_xml/>
1184 </assert_contents> 1233 </assert_contents>
1185 </output> 1234 </output>
1235 <assert_stdout>
1236 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1237 </assert_stdout>
1186 </test> 1238 </test>
1187 <!-- TOPP_IDFileConverter_19 --> 1239 <!-- TOPP_IDFileConverter_19 -->
1188 <test expect_num_outputs="2"> 1240 <test expect_num_outputs="2">
1189 <section name="adv_opts"> 1241 <section name="adv_opts">
1190 <param name="ignore_proteins_per_peptide" value="false"/> 1242 <param name="ignore_proteins_per_peptide" value="false"/>
1196 <param name="number_of_hits" value="1"/> 1248 <param name="number_of_hits" value="1"/>
1197 <param name="force" value="false"/> 1249 <param name="force" value="false"/>
1198 <param name="test" value="true"/> 1250 <param name="test" value="true"/>
1199 </section> 1251 </section>
1200 <param name="in" value="IDFileConverter_19_input.idXML"/> 1252 <param name="in" value="IDFileConverter_19_input.idXML"/>
1201 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> 1253 <output name="out" value="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
1202 <param name="out_type" value="pepXML"/> 1254 <param name="out_type" value="pepXML"/>
1203 <param name="mz_name" value=""/> 1255 <param name="mz_name" value=""/>
1204 <param name="peptideprophet_analyzed" value="false"/> 1256 <param name="peptideprophet_analyzed" value="false"/>
1205 <param name="score_type" value="qvalue"/> 1257 <param name="score_type" value="qvalue"/>
1206 <section name="fasta_to_mzml"> 1258 <section name="fasta_to_mzml">
1240 <output name="ctd_out" ftype="xml"> 1292 <output name="ctd_out" ftype="xml">
1241 <assert_contents> 1293 <assert_contents>
1242 <is_valid_xml/> 1294 <is_valid_xml/>
1243 </assert_contents> 1295 </assert_contents>
1244 </output> 1296 </output>
1297 <assert_stdout>
1298 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1299 </assert_stdout>
1245 </test> 1300 </test>
1246 <!-- TOPP_IDFileConverter_20 --> 1301 <!-- TOPP_IDFileConverter_20 -->
1247 <test expect_num_outputs="2"> 1302 <test expect_num_outputs="2">
1248 <section name="adv_opts"> 1303 <section name="adv_opts">
1249 <param name="ignore_proteins_per_peptide" value="false"/> 1304 <param name="ignore_proteins_per_peptide" value="false"/>
1255 <param name="number_of_hits" value="1"/> 1310 <param name="number_of_hits" value="1"/>
1256 <param name="force" value="false"/> 1311 <param name="force" value="false"/>
1257 <param name="test" value="true"/> 1312 <param name="test" value="true"/>
1258 </section> 1313 </section>
1259 <param name="in" value="IDFileConverter_20_input.idXML"/> 1314 <param name="in" value="IDFileConverter_20_input.idXML"/>
1260 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> 1315 <output name="out" value="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
1261 <param name="out_type" value="pepXML"/> 1316 <param name="out_type" value="pepXML"/>
1262 <param name="mz_name" value=""/> 1317 <param name="mz_name" value=""/>
1263 <param name="peptideprophet_analyzed" value="false"/> 1318 <param name="peptideprophet_analyzed" value="false"/>
1264 <param name="score_type" value="qvalue"/> 1319 <param name="score_type" value="qvalue"/>
1265 <section name="fasta_to_mzml"> 1320 <section name="fasta_to_mzml">
1299 <output name="ctd_out" ftype="xml"> 1354 <output name="ctd_out" ftype="xml">
1300 <assert_contents> 1355 <assert_contents>
1301 <is_valid_xml/> 1356 <is_valid_xml/>
1302 </assert_contents> 1357 </assert_contents>
1303 </output> 1358 </output>
1359 <assert_stdout>
1360 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1361 </assert_stdout>
1304 </test> 1362 </test>
1305 <!-- TOPP_IDFileConverter_21 --> 1363 <!-- TOPP_IDFileConverter_21 -->
1306 <test expect_num_outputs="2"> 1364 <test expect_num_outputs="2">
1307 <section name="adv_opts"> 1365 <section name="adv_opts">
1308 <param name="ignore_proteins_per_peptide" value="false"/> 1366 <param name="ignore_proteins_per_peptide" value="false"/>
1314 <param name="number_of_hits" value="1"/> 1372 <param name="number_of_hits" value="1"/>
1315 <param name="force" value="false"/> 1373 <param name="force" value="false"/>
1316 <param name="test" value="true"/> 1374 <param name="test" value="true"/>
1317 </section> 1375 </section>
1318 <param name="in" value="IDFileConverter_21_input.idXML"/> 1376 <param name="in" value="IDFileConverter_21_input.idXML"/>
1319 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1377 <output name="out" value="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1320 <param name="out_type" value="idXML"/> 1378 <param name="out_type" value="idXML"/>
1321 <param name="mz_file" value="IDMapper_4_input.mzML"/> 1379 <param name="mz_file" value="IDMapper_4_input.mzML"/>
1322 <param name="mz_name" value=""/> 1380 <param name="mz_name" value=""/>
1323 <param name="peptideprophet_analyzed" value="false"/> 1381 <param name="peptideprophet_analyzed" value="false"/>
1324 <param name="score_type" value="qvalue"/> 1382 <param name="score_type" value="qvalue"/>
1359 <output name="ctd_out" ftype="xml"> 1417 <output name="ctd_out" ftype="xml">
1360 <assert_contents> 1418 <assert_contents>
1361 <is_valid_xml/> 1419 <is_valid_xml/>
1362 </assert_contents> 1420 </assert_contents>
1363 </output> 1421 </output>
1422 <assert_stdout>
1423 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1424 </assert_stdout>
1364 </test> 1425 </test>
1365 <!-- TOPP_IDFileConverter_22 --> 1426 <!-- TOPP_IDFileConverter_22 -->
1366 <test expect_num_outputs="2"> 1427 <test expect_num_outputs="2">
1367 <section name="adv_opts"> 1428 <section name="adv_opts">
1368 <param name="ignore_proteins_per_peptide" value="false"/> 1429 <param name="ignore_proteins_per_peptide" value="false"/>
1374 <param name="number_of_hits" value="1"/> 1435 <param name="number_of_hits" value="1"/>
1375 <param name="force" value="false"/> 1436 <param name="force" value="false"/>
1376 <param name="test" value="true"/> 1437 <param name="test" value="true"/>
1377 </section> 1438 </section>
1378 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> 1439 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
1379 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1440 <output name="out" value="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1380 <param name="out_type" value="idXML"/> 1441 <param name="out_type" value="idXML"/>
1381 <param name="mz_file" value="spectra.mzML"/> 1442 <param name="mz_file" value="spectra.mzML"/>
1382 <param name="mz_name" value=""/> 1443 <param name="mz_name" value=""/>
1383 <param name="peptideprophet_analyzed" value="false"/> 1444 <param name="peptideprophet_analyzed" value="false"/>
1384 <param name="score_type" value="qvalue"/> 1445 <param name="score_type" value="qvalue"/>
1419 <output name="ctd_out" ftype="xml"> 1480 <output name="ctd_out" ftype="xml">
1420 <assert_contents> 1481 <assert_contents>
1421 <is_valid_xml/> 1482 <is_valid_xml/>
1422 </assert_contents> 1483 </assert_contents>
1423 </output> 1484 </output>
1485 <assert_stdout>
1486 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1487 </assert_stdout>
1424 </test> 1488 </test>
1425 <!-- TOPP_IDFileConverter_23 --> 1489 <!-- TOPP_IDFileConverter_23 -->
1426 <test expect_num_outputs="2"> 1490 <test expect_num_outputs="2">
1427 <section name="adv_opts"> 1491 <section name="adv_opts">
1428 <param name="ignore_proteins_per_peptide" value="false"/> 1492 <param name="ignore_proteins_per_peptide" value="false"/>
1434 <param name="number_of_hits" value="1"/> 1498 <param name="number_of_hits" value="1"/>
1435 <param name="force" value="false"/> 1499 <param name="force" value="false"/>
1436 <param name="test" value="true"/> 1500 <param name="test" value="true"/>
1437 </section> 1501 </section>
1438 <param name="in" value="IDFileConverter_23_input.mzid"/> 1502 <param name="in" value="IDFileConverter_23_input.mzid"/>
1439 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1503 <output name="out" value="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1440 <param name="out_type" value="idXML"/> 1504 <param name="out_type" value="idXML"/>
1441 <param name="mz_name" value=""/> 1505 <param name="mz_name" value=""/>
1442 <param name="peptideprophet_analyzed" value="false"/> 1506 <param name="peptideprophet_analyzed" value="false"/>
1443 <param name="score_type" value="qvalue"/> 1507 <param name="score_type" value="qvalue"/>
1444 <section name="fasta_to_mzml"> 1508 <section name="fasta_to_mzml">
1478 <output name="ctd_out" ftype="xml"> 1542 <output name="ctd_out" ftype="xml">
1479 <assert_contents> 1543 <assert_contents>
1480 <is_valid_xml/> 1544 <is_valid_xml/>
1481 </assert_contents> 1545 </assert_contents>
1482 </output> 1546 </output>
1547 <assert_stdout>
1548 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1549 </assert_stdout>
1483 </test> 1550 </test>
1484 <!-- TOPP_IDFileConverter_24 --> 1551 <!-- TOPP_IDFileConverter_24 -->
1485 <test expect_num_outputs="2"> 1552 <test expect_num_outputs="2">
1486 <section name="adv_opts"> 1553 <section name="adv_opts">
1487 <param name="ignore_proteins_per_peptide" value="false"/> 1554 <param name="ignore_proteins_per_peptide" value="false"/>
1493 <param name="number_of_hits" value="1"/> 1560 <param name="number_of_hits" value="1"/>
1494 <param name="force" value="false"/> 1561 <param name="force" value="false"/>
1495 <param name="test" value="true"/> 1562 <param name="test" value="true"/>
1496 </section> 1563 </section>
1497 <param name="in" value="IDFileConverter_24_input.pep.xml"/> 1564 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
1498 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1565 <output name="out" value="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1499 <param name="out_type" value="idXML"/> 1566 <param name="out_type" value="idXML"/>
1500 <param name="mz_name" value=""/> 1567 <param name="mz_name" value=""/>
1501 <param name="peptideprophet_analyzed" value="false"/> 1568 <param name="peptideprophet_analyzed" value="false"/>
1502 <param name="score_type" value="qvalue"/> 1569 <param name="score_type" value="qvalue"/>
1503 <section name="fasta_to_mzml"> 1570 <section name="fasta_to_mzml">
1537 <output name="ctd_out" ftype="xml"> 1604 <output name="ctd_out" ftype="xml">
1538 <assert_contents> 1605 <assert_contents>
1539 <is_valid_xml/> 1606 <is_valid_xml/>
1540 </assert_contents> 1607 </assert_contents>
1541 </output> 1608 </output>
1609 <assert_stdout>
1610 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1611 </assert_stdout>
1542 </test> 1612 </test>
1543 <!-- TOPP_IDFileConverter_25 --> 1613 <!-- TOPP_IDFileConverter_25 -->
1544 <test expect_num_outputs="2"> 1614 <test expect_num_outputs="2">
1545 <section name="adv_opts"> 1615 <section name="adv_opts">
1546 <param name="ignore_proteins_per_peptide" value="false"/> 1616 <param name="ignore_proteins_per_peptide" value="false"/>
1552 <param name="number_of_hits" value="1"/> 1622 <param name="number_of_hits" value="1"/>
1553 <param name="force" value="false"/> 1623 <param name="force" value="false"/>
1554 <param name="test" value="true"/> 1624 <param name="test" value="true"/>
1555 </section> 1625 </section>
1556 <param name="in" value="IDFileConverter_25_input.idXML"/> 1626 <param name="in" value="IDFileConverter_25_input.idXML"/>
1557 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> 1627 <output name="out" value="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
1558 <param name="out_type" value="pepXML"/> 1628 <param name="out_type" value="pepXML"/>
1559 <param name="mz_name" value=""/> 1629 <param name="mz_name" value=""/>
1560 <param name="peptideprophet_analyzed" value="false"/> 1630 <param name="peptideprophet_analyzed" value="false"/>
1561 <param name="score_type" value="qvalue"/> 1631 <param name="score_type" value="qvalue"/>
1562 <section name="fasta_to_mzml"> 1632 <section name="fasta_to_mzml">
1596 <output name="ctd_out" ftype="xml"> 1666 <output name="ctd_out" ftype="xml">
1597 <assert_contents> 1667 <assert_contents>
1598 <is_valid_xml/> 1668 <is_valid_xml/>
1599 </assert_contents> 1669 </assert_contents>
1600 </output> 1670 </output>
1671 <assert_stdout>
1672 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1673 </assert_stdout>
1601 </test> 1674 </test>
1602 <!-- TOPP_IDFileConverter_26 --> 1675 <!-- TOPP_IDFileConverter_26 -->
1603 <test expect_num_outputs="2"> 1676 <test expect_num_outputs="2">
1604 <section name="adv_opts"> 1677 <section name="adv_opts">
1605 <param name="ignore_proteins_per_peptide" value="false"/> 1678 <param name="ignore_proteins_per_peptide" value="false"/>
1611 <param name="number_of_hits" value="1"/> 1684 <param name="number_of_hits" value="1"/>
1612 <param name="force" value="false"/> 1685 <param name="force" value="false"/>
1613 <param name="test" value="true"/> 1686 <param name="test" value="true"/>
1614 </section> 1687 </section>
1615 <param name="in" value="IDFileConverter_26_input.mzid"/> 1688 <param name="in" value="IDFileConverter_26_input.mzid"/>
1616 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1689 <output name="out" value="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1617 <param name="out_type" value="idXML"/> 1690 <param name="out_type" value="idXML"/>
1618 <param name="mz_name" value=""/> 1691 <param name="mz_name" value=""/>
1619 <param name="peptideprophet_analyzed" value="false"/> 1692 <param name="peptideprophet_analyzed" value="false"/>
1620 <param name="score_type" value="qvalue"/> 1693 <param name="score_type" value="qvalue"/>
1621 <section name="fasta_to_mzml"> 1694 <section name="fasta_to_mzml">
1655 <output name="ctd_out" ftype="xml"> 1728 <output name="ctd_out" ftype="xml">
1656 <assert_contents> 1729 <assert_contents>
1657 <is_valid_xml/> 1730 <is_valid_xml/>
1658 </assert_contents> 1731 </assert_contents>
1659 </output> 1732 </output>
1733 <assert_stdout>
1734 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1735 </assert_stdout>
1660 </test> 1736 </test>
1661 <!-- TOPP_IDFileConverter_27 --> 1737 <!-- TOPP_IDFileConverter_27 -->
1662 <test expect_num_outputs="2"> 1738 <test expect_num_outputs="2">
1663 <section name="adv_opts"> 1739 <section name="adv_opts">
1664 <param name="ignore_proteins_per_peptide" value="false"/> 1740 <param name="ignore_proteins_per_peptide" value="false"/>
1670 <param name="number_of_hits" value="1"/> 1746 <param name="number_of_hits" value="1"/>
1671 <param name="force" value="false"/> 1747 <param name="force" value="false"/>
1672 <param name="test" value="true"/> 1748 <param name="test" value="true"/>
1673 </section> 1749 </section>
1674 <param name="in" value="IDFileConverter_27_input.idXML"/> 1750 <param name="in" value="IDFileConverter_27_input.idXML"/>
1675 <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 1751 <output name="out" value="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
1676 <param name="out_type" value="fasta"/> 1752 <param name="out_type" value="fasta"/>
1677 <param name="mz_name" value=""/> 1753 <param name="mz_name" value=""/>
1678 <param name="peptideprophet_analyzed" value="false"/> 1754 <param name="peptideprophet_analyzed" value="false"/>
1679 <param name="score_type" value="qvalue"/> 1755 <param name="score_type" value="qvalue"/>
1680 <section name="fasta_to_mzml"> 1756 <section name="fasta_to_mzml">
1714 <output name="ctd_out" ftype="xml"> 1790 <output name="ctd_out" ftype="xml">
1715 <assert_contents> 1791 <assert_contents>
1716 <is_valid_xml/> 1792 <is_valid_xml/>
1717 </assert_contents> 1793 </assert_contents>
1718 </output> 1794 </output>
1795 <assert_stdout>
1796 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1797 </assert_stdout>
1719 </test> 1798 </test>
1720 <!-- TOPP_IDFileConverter_28 --> 1799 <!-- TOPP_IDFileConverter_28 -->
1721 <test expect_num_outputs="2"> 1800 <test expect_num_outputs="2">
1722 <section name="adv_opts"> 1801 <section name="adv_opts">
1723 <param name="ignore_proteins_per_peptide" value="false"/> 1802 <param name="ignore_proteins_per_peptide" value="false"/>
1729 <param name="number_of_hits" value="-1"/> 1808 <param name="number_of_hits" value="-1"/>
1730 <param name="force" value="false"/> 1809 <param name="force" value="false"/>
1731 <param name="test" value="true"/> 1810 <param name="test" value="true"/>
1732 </section> 1811 </section>
1733 <param name="in" value="IDFileConverter_27_input.idXML"/> 1812 <param name="in" value="IDFileConverter_27_input.idXML"/>
1734 <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 1813 <output name="out" value="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
1735 <param name="out_type" value="fasta"/> 1814 <param name="out_type" value="fasta"/>
1736 <param name="mz_name" value=""/> 1815 <param name="mz_name" value=""/>
1737 <param name="peptideprophet_analyzed" value="false"/> 1816 <param name="peptideprophet_analyzed" value="false"/>
1738 <param name="score_type" value="qvalue"/> 1817 <param name="score_type" value="qvalue"/>
1739 <section name="fasta_to_mzml"> 1818 <section name="fasta_to_mzml">
1773 <output name="ctd_out" ftype="xml"> 1852 <output name="ctd_out" ftype="xml">
1774 <assert_contents> 1853 <assert_contents>
1775 <is_valid_xml/> 1854 <is_valid_xml/>
1776 </assert_contents> 1855 </assert_contents>
1777 </output> 1856 </output>
1857 <assert_stdout>
1858 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1859 </assert_stdout>
1778 </test> 1860 </test>
1779 <!-- TOPP_IDFileConverter_29 --> 1861 <!-- TOPP_IDFileConverter_29 -->
1780 <test expect_num_outputs="2"> 1862 <test expect_num_outputs="2">
1781 <section name="adv_opts"> 1863 <section name="adv_opts">
1782 <param name="ignore_proteins_per_peptide" value="false"/> 1864 <param name="ignore_proteins_per_peptide" value="false"/>
1788 <param name="number_of_hits" value="1"/> 1870 <param name="number_of_hits" value="1"/>
1789 <param name="force" value="false"/> 1871 <param name="force" value="false"/>
1790 <param name="test" value="true"/> 1872 <param name="test" value="true"/>
1791 </section> 1873 </section>
1792 <param name="in" value="IDFileConverter_27_input.idXML"/> 1874 <param name="in" value="IDFileConverter_27_input.idXML"/>
1793 <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 1875 <output name="out" value="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
1794 <param name="out_type" value="fasta"/> 1876 <param name="out_type" value="fasta"/>
1795 <param name="mz_name" value=""/> 1877 <param name="mz_name" value=""/>
1796 <param name="peptideprophet_analyzed" value="false"/> 1878 <param name="peptideprophet_analyzed" value="false"/>
1797 <param name="score_type" value="qvalue"/> 1879 <param name="score_type" value="qvalue"/>
1798 <section name="fasta_to_mzml"> 1880 <section name="fasta_to_mzml">
1832 <output name="ctd_out" ftype="xml"> 1914 <output name="ctd_out" ftype="xml">
1833 <assert_contents> 1915 <assert_contents>
1834 <is_valid_xml/> 1916 <is_valid_xml/>
1835 </assert_contents> 1917 </assert_contents>
1836 </output> 1918 </output>
1919 <assert_stdout>
1920 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1921 </assert_stdout>
1837 </test> 1922 </test>
1838 <!-- TOPP_IDFileConverter_30 --> 1923 <!-- TOPP_IDFileConverter_30 -->
1839 <test expect_num_outputs="2"> 1924 <test expect_num_outputs="2">
1840 <section name="adv_opts"> 1925 <section name="adv_opts">
1841 <param name="ignore_proteins_per_peptide" value="false"/> 1926 <param name="ignore_proteins_per_peptide" value="false"/>
1847 <param name="number_of_hits" value="2"/> 1932 <param name="number_of_hits" value="2"/>
1848 <param name="force" value="false"/> 1933 <param name="force" value="false"/>
1849 <param name="test" value="true"/> 1934 <param name="test" value="true"/>
1850 </section> 1935 </section>
1851 <param name="in" value="IDFileConverter_27_input.idXML"/> 1936 <param name="in" value="IDFileConverter_27_input.idXML"/>
1852 <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 1937 <output name="out" value="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
1853 <param name="out_type" value="fasta"/> 1938 <param name="out_type" value="fasta"/>
1854 <param name="mz_name" value=""/> 1939 <param name="mz_name" value=""/>
1855 <param name="peptideprophet_analyzed" value="false"/> 1940 <param name="peptideprophet_analyzed" value="false"/>
1856 <param name="score_type" value="qvalue"/> 1941 <param name="score_type" value="qvalue"/>
1857 <section name="fasta_to_mzml"> 1942 <section name="fasta_to_mzml">
1891 <output name="ctd_out" ftype="xml"> 1976 <output name="ctd_out" ftype="xml">
1892 <assert_contents> 1977 <assert_contents>
1893 <is_valid_xml/> 1978 <is_valid_xml/>
1894 </assert_contents> 1979 </assert_contents>
1895 </output> 1980 </output>
1981 <assert_stdout>
1982 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
1983 </assert_stdout>
1896 </test> 1984 </test>
1897 <!-- TOPP_IDFileConverter_31 --> 1985 <!-- TOPP_IDFileConverter_31 -->
1898 <test expect_num_outputs="2"> 1986 <test expect_num_outputs="2">
1899 <section name="adv_opts"> 1987 <section name="adv_opts">
1900 <param name="ignore_proteins_per_peptide" value="false"/> 1988 <param name="ignore_proteins_per_peptide" value="false"/>
1906 <param name="number_of_hits" value="1"/> 1994 <param name="number_of_hits" value="1"/>
1907 <param name="force" value="false"/> 1995 <param name="force" value="false"/>
1908 <param name="test" value="true"/> 1996 <param name="test" value="true"/>
1909 </section> 1997 </section>
1910 <param name="in" value="IDFileConverter_31_input.mzid"/> 1998 <param name="in" value="IDFileConverter_31_input.mzid"/>
1911 <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 1999 <output name="out" value="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
1912 <param name="out_type" value="idXML"/> 2000 <param name="out_type" value="idXML"/>
1913 <param name="mz_name" value=""/> 2001 <param name="mz_name" value=""/>
1914 <param name="peptideprophet_analyzed" value="false"/> 2002 <param name="peptideprophet_analyzed" value="false"/>
1915 <param name="score_type" value="qvalue"/> 2003 <param name="score_type" value="qvalue"/>
1916 <section name="fasta_to_mzml"> 2004 <section name="fasta_to_mzml">
1950 <output name="ctd_out" ftype="xml"> 2038 <output name="ctd_out" ftype="xml">
1951 <assert_contents> 2039 <assert_contents>
1952 <is_valid_xml/> 2040 <is_valid_xml/>
1953 </assert_contents> 2041 </assert_contents>
1954 </output> 2042 </output>
2043 <assert_stdout>
2044 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
2045 </assert_stdout>
1955 </test> 2046 </test>
1956 <!-- TOPP_IDFileConverter_32 --> 2047 <!-- TOPP_IDFileConverter_32 -->
1957 <test expect_num_outputs="2"> 2048 <test expect_num_outputs="2">
1958 <section name="adv_opts"> 2049 <section name="adv_opts">
1959 <param name="ignore_proteins_per_peptide" value="false"/> 2050 <param name="ignore_proteins_per_peptide" value="false"/>
1965 <param name="number_of_hits" value="1"/> 2056 <param name="number_of_hits" value="1"/>
1966 <param name="force" value="false"/> 2057 <param name="force" value="false"/>
1967 <param name="test" value="true"/> 2058 <param name="test" value="true"/>
1968 </section> 2059 </section>
1969 <param name="in" value="IDFileConverter_32_input.FASTA"/> 2060 <param name="in" value="IDFileConverter_32_input.FASTA"/>
1970 <output name="out" file="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/> 2061 <output name="out" value="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
1971 <param name="out_type" value="mzML"/> 2062 <param name="out_type" value="mzML"/>
1972 <param name="mz_name" value=""/> 2063 <param name="mz_name" value=""/>
1973 <param name="peptideprophet_analyzed" value="false"/> 2064 <param name="peptideprophet_analyzed" value="false"/>
1974 <param name="score_type" value="qvalue"/> 2065 <param name="score_type" value="qvalue"/>
1975 <section name="fasta_to_mzml"> 2066 <section name="fasta_to_mzml">
2009 <output name="ctd_out" ftype="xml"> 2100 <output name="ctd_out" ftype="xml">
2010 <assert_contents> 2101 <assert_contents>
2011 <is_valid_xml/> 2102 <is_valid_xml/>
2012 </assert_contents> 2103 </assert_contents>
2013 </output> 2104 </output>
2105 <assert_stdout>
2106 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
2107 </assert_stdout>
2014 </test> 2108 </test>
2015 <!-- TOPP_IDFileConverter_33 --> 2109 <!-- TOPP_IDFileConverter_33 -->
2016 <test expect_num_outputs="2"> 2110 <test expect_num_outputs="2">
2017 <section name="adv_opts"> 2111 <section name="adv_opts">
2018 <param name="ignore_proteins_per_peptide" value="false"/> 2112 <param name="ignore_proteins_per_peptide" value="false"/>
2024 <param name="number_of_hits" value="1"/> 2118 <param name="number_of_hits" value="1"/>
2025 <param name="force" value="false"/> 2119 <param name="force" value="false"/>
2026 <param name="test" value="true"/> 2120 <param name="test" value="true"/>
2027 </section> 2121 </section>
2028 <param name="in" value="IDFileConverter_32_input.FASTA"/> 2122 <param name="in" value="IDFileConverter_32_input.FASTA"/>
2029 <output name="out" file="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/> 2123 <output name="out" value="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
2030 <param name="out_type" value="mzML"/> 2124 <param name="out_type" value="mzML"/>
2031 <param name="mz_name" value=""/> 2125 <param name="mz_name" value=""/>
2032 <param name="peptideprophet_analyzed" value="false"/> 2126 <param name="peptideprophet_analyzed" value="false"/>
2033 <param name="score_type" value="qvalue"/> 2127 <param name="score_type" value="qvalue"/>
2034 <section name="fasta_to_mzml"> 2128 <section name="fasta_to_mzml">
2068 <output name="ctd_out" ftype="xml"> 2162 <output name="ctd_out" ftype="xml">
2069 <assert_contents> 2163 <assert_contents>
2070 <is_valid_xml/> 2164 <is_valid_xml/>
2071 </assert_contents> 2165 </assert_contents>
2072 </output> 2166 </output>
2167 <assert_stdout>
2168 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
2169 </assert_stdout>
2073 </test> 2170 </test>
2074 <!-- TOPP_IDFileConverter_34_1 --> 2171 <!-- TOPP_IDFileConverter_34_1 -->
2075 <test expect_num_outputs="2"> 2172 <test expect_num_outputs="2">
2076 <section name="adv_opts"> 2173 <section name="adv_opts">
2077 <param name="ignore_proteins_per_peptide" value="false"/> 2174 <param name="ignore_proteins_per_peptide" value="false"/>
2083 <param name="number_of_hits" value="1"/> 2180 <param name="number_of_hits" value="1"/>
2084 <param name="force" value="false"/> 2181 <param name="force" value="false"/>
2085 <param name="test" value="true"/> 2182 <param name="test" value="true"/>
2086 </section> 2183 </section>
2087 <param name="in" value="IDFileConverter_34_input.idXML"/> 2184 <param name="in" value="IDFileConverter_34_input.idXML"/>
2088 <output name="out" file="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> 2185 <output name="out" value="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
2089 <param name="out_type" value="oms"/> 2186 <param name="out_type" value="oms"/>
2090 <param name="mz_name" value=""/> 2187 <param name="mz_name" value=""/>
2091 <param name="peptideprophet_analyzed" value="false"/> 2188 <param name="peptideprophet_analyzed" value="false"/>
2092 <param name="score_type" value="qvalue"/> 2189 <param name="score_type" value="qvalue"/>
2093 <section name="fasta_to_mzml"> 2190 <section name="fasta_to_mzml">
2127 <output name="ctd_out" ftype="xml"> 2224 <output name="ctd_out" ftype="xml">
2128 <assert_contents> 2225 <assert_contents>
2129 <is_valid_xml/> 2226 <is_valid_xml/>
2130 </assert_contents> 2227 </assert_contents>
2131 </output> 2228 </output>
2229 <assert_stdout>
2230 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
2231 </assert_stdout>
2132 </test> 2232 </test>
2133 <!-- TOPP_IDFileConverter_34_2 --> 2233 <!-- TOPP_IDFileConverter_34_2 -->
2134 <test expect_num_outputs="2"> 2234 <test expect_num_outputs="2">
2135 <section name="adv_opts"> 2235 <section name="adv_opts">
2136 <param name="ignore_proteins_per_peptide" value="false"/> 2236 <param name="ignore_proteins_per_peptide" value="false"/>
2142 <param name="number_of_hits" value="1"/> 2242 <param name="number_of_hits" value="1"/>
2143 <param name="force" value="false"/> 2243 <param name="force" value="false"/>
2144 <param name="test" value="true"/> 2244 <param name="test" value="true"/>
2145 </section> 2245 </section>
2146 <param name="in" value="IDFileConverter_34_output1.oms"/> 2246 <param name="in" value="IDFileConverter_34_output1.oms"/>
2147 <output name="out" file="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 2247 <output name="out" value="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
2148 <param name="out_type" value="idXML"/> 2248 <param name="out_type" value="idXML"/>
2149 <param name="mz_name" value=""/> 2249 <param name="mz_name" value=""/>
2150 <param name="peptideprophet_analyzed" value="false"/> 2250 <param name="peptideprophet_analyzed" value="false"/>
2151 <param name="score_type" value="qvalue"/> 2251 <param name="score_type" value="qvalue"/>
2152 <section name="fasta_to_mzml"> 2252 <section name="fasta_to_mzml">
2186 <output name="ctd_out" ftype="xml"> 2286 <output name="ctd_out" ftype="xml">
2187 <assert_contents> 2287 <assert_contents>
2188 <is_valid_xml/> 2288 <is_valid_xml/>
2189 </assert_contents> 2289 </assert_contents>
2190 </output> 2290 </output>
2291 <assert_stdout>
2292 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
2293 </assert_stdout>
2191 </test> 2294 </test>
2192 </tests> 2295 </tests>
2193 <help><![CDATA[Converts identification engine file formats. 2296 <help><![CDATA[Converts identification engine file formats.
2194 2297
2195 2298
2196 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFileConverter.html]]></help> 2299 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFileConverter.html]]></help>
2197 <expand macro="references"/> 2300 <expand macro="references"/>
2198 </tool> 2301 </tool>