Mercurial > repos > galaxyp > openms_idfileconverter

annotate IDFileConverter.xml @ 15:7d0eb300f360 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:01:16 +0000
parents 250d6a43f66b
children 5e9c35b8d194
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Converts identification engine file formats.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDFileConverter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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20 #if $mz_file:
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21 mkdir mz_file &&
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22 ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
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23 #end if
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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33 -out
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34 'out/output.${out_type}'
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35 #if $mz_file:
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36 -mz_file
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37 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)'
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38 #end if
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40 ## Postprocessing
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41 && mv 'out/output.${out_type}' '$out'
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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44 #end if]]></command>
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45 <configfiles>
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46 <inputs name="args_json" data_style="paths"/>
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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48 </configfiles>
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49 <inputs>
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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)"/>
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51 <param argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
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52 <option value="fasta">fasta</option>
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53 <option value="idXML">idxml</option>
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54 <option value="mzML">mzml</option>
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55 <option value="mzid">mzid</option>
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56 <option value="oms">sqlite (oms)</option>
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57 <option value="pepXML">pepxml</option>
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58 <option value="xquest.xml">xquest.xml</option>
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59 <expand macro="list_string_san" name="out_type"/>
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60 </param>
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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)"/>
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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'">
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63 <expand macro="list_string_san" name="mz_name"/>
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64 </param>
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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"/>
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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="">
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67 <option value="qvalue" selected="true">qvalue</option>
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68 <option value="PEP">PEP</option>
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69 <option value="score">score</option>
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70 <expand macro="list_string_san" name="score_type"/>
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71 </param>
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72 <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
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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">
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74 <option value="none" selected="true">none</option>
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75 <option value="coarse">coarse</option>
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76 <option value="fine">fine</option>
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77 <expand macro="list_string_san" name="isotope_model"/>
0
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78 </param>
15
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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86 <param name="add_abundant_immonium_ions" argument="-fasta_to_mzml:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/>
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87 <param name="add_first_prefix_ion" argument="-fasta_to_mzml:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
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88 <param name="add_y_ions" argument="-fasta_to_mzml:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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104 <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" optional="true" label="Enzym used to digest the fasta proteins" help="">
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105 <option value="Trypsin" selected="true">Trypsin</option>
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106 <option value="Chymotrypsin">Chymotrypsin</option>
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107 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
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108 <option value="CNBr">CNBr</option>
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109 <option value="Formic_acid">Formic_acid</option>
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110 <option value="leukocyte elastase">leukocyte elastase</option>
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111 <option value="proline endopeptidase">proline endopeptidase</option>
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112 <option value="Arg-C/P">Arg-C/P</option>
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113 <option value="Asp-N">Asp-N</option>
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114 <option value="Asp-N/B">Asp-N/B</option>
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115 <option value="Asp-N_ambic">Asp-N_ambic</option>
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116 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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117 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
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118 <option value="2-iodobenzoate">2-iodobenzoate</option>
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119 <option value="iodosobenzoate">iodosobenzoate</option>
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120 <option value="cyanogen-bromide">cyanogen-bromide</option>
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121 <option value="Clostripain/P">Clostripain/P</option>
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122 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
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123 <option value="no cleavage">no cleavage</option>
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124 <option value="unspecific cleavage">unspecific cleavage</option>
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125 <option value="Lys-C">Lys-C</option>
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126 <option value="Lys-N">Lys-N</option>
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127 <option value="Lys-C/P">Lys-C/P</option>
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128 <option value="PepsinA">PepsinA</option>
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129 <option value="TrypChymo">TrypChymo</option>
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130 <option value="Trypsin/P">Trypsin/P</option>
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131 <option value="V8-DE">V8-DE</option>
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132 <option value="V8-E">V8-E</option>
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133 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
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134 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
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135 <option value="Glu-C+P">Glu-C+P</option>
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136 <option value="PepsinA + P">PepsinA + P</option>
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137 <option value="Arg-C">Arg-C</option>
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138 <expand macro="list_string_san" name="enzyme"/>
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139 </param>
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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=""/>
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141 <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" optional="true" value="1" label="Minimum charge" help=""/>
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142 <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" optional="true" value="1" label="Maximum charge" help=""/>
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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)"/>
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144 </section>
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145 <expand macro="adv_opts_macro">
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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)"/>
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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">
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148 <expand macro="list_string_san" name="scan_regex"/>
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149 </param>
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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"/>
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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=""/>
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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"/>
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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=""/>
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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"/>
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155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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157 <expand macro="list_string_san" name="test"/>
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158 </param>
0
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159 </expand>
13
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160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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161 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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162 </param>
0
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163 </inputs>
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164 <outputs>
15
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165 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta">
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166 <change_format>
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167 <when input="out_type" value="idXML" format="idxml"/>
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168 <when input="out_type" value="mzML" format="mzml"/>
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169 <when input="out_type" value="mzid" format="mzid"/>
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170 <when input="out_type" value="oms" format="sqlite"/>
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171 <when input="out_type" value="pepXML" format="pepxml"/>
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172 <when input="out_type" value="xquest.xml" format="xquest.xml"/>
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173 </change_format>
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174 </data>
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175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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177 </data>
0
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178 </outputs>
15
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179 <tests><!-- TOPP_IDFileConverter_1 -->
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180 <test expect_num_outputs="2">
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181 <section name="adv_opts">
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182 <param name="ignore_proteins_per_peptide" value="false"/>
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183 <param name="scan_regex" value=""/>
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184 <param name="no_spectra_data_override" value="false"/>
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185 <param name="no_spectra_references_override" value="false"/>
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186 <param name="add_ionmatch_annotation" value="0.0"/>
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187 <param name="concatenate_peptides" value="false"/>
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188 <param name="number_of_hits" value="1"/>
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189 <param name="force" value="false"/>
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190 <param name="test" value="true"/>
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191 </section>
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192 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
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193 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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194 <param name="out_type" value="idXML"/>
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195 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
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196 <param name="mz_name" value=""/>
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197 <param name="peptideprophet_analyzed" value="false"/>
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198 <param name="score_type" value="qvalue"/>
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199 <section name="fasta_to_mzml">
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200 <param name="isotope_model" value="none"/>
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201 <param name="max_isotope" value="2"/>
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202 <param name="max_isotope_probability" value="0.05"/>
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203 <param name="add_metainfo" value="false"/>
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204 <param name="add_losses" value="false"/>
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205 <param name="sort_by_position" value="true"/>
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206 <param name="add_precursor_peaks" value="false"/>
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207 <param name="add_all_precursor_charges" value="false"/>
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208 <param name="add_abundant_immonium_ions" value="false"/>
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209 <param name="add_first_prefix_ion" value="false"/>
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210 <param name="add_y_ions" value="true"/>
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211 <param name="add_b_ions" value="true"/>
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212 <param name="add_a_ions" value="false"/>
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213 <param name="add_c_ions" value="false"/>
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214 <param name="add_x_ions" value="false"/>
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215 <param name="add_z_ions" value="false"/>
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216 <param name="y_intensity" value="1.0"/>
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217 <param name="b_intensity" value="1.0"/>
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218 <param name="a_intensity" value="1.0"/>
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219 <param name="c_intensity" value="1.0"/>
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220 <param name="x_intensity" value="1.0"/>
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221 <param name="z_intensity" value="1.0"/>
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222 <param name="relative_loss_intensity" value="0.1"/>
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223 <param name="precursor_intensity" value="1.0"/>
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224 <param name="precursor_H2O_intensity" value="1.0"/>
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225 <param name="precursor_NH3_intensity" value="1.0"/>
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226 <param name="enzyme" value="Trypsin"/>
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227 <param name="missed_cleavages" value="0"/>
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228 <param name="min_charge" value="1"/>
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229 <param name="max_charge" value="1"/>
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230 <param name="precursor_charge" value="0"/>
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231 </section>
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232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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233 <output name="ctd_out" ftype="xml">
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234 <assert_contents>
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235 <is_valid_xml/>
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236 </assert_contents>
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237 </output>
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238 </test>
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239 <!-- TOPP_IDFileConverter_2 -->
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240 <test expect_num_outputs="2">
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241 <section name="adv_opts">
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242 <param name="ignore_proteins_per_peptide" value="false"/>
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243 <param name="scan_regex" value=""/>
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244 <param name="no_spectra_data_override" value="false"/>
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245 <param name="no_spectra_references_override" value="false"/>
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246 <param name="add_ionmatch_annotation" value="0.0"/>
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247 <param name="concatenate_peptides" value="false"/>
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248 <param name="number_of_hits" value="1"/>
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249 <param name="force" value="false"/>
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250 <param name="test" value="true"/>
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251 </section>
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252 <param name="in" value="PepXMLFile_test.pepxml"/>
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253 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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254 <param name="out_type" value="idXML"/>
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255 <param name="mz_file" value="PepXMLFile_test.mzML"/>
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256 <param name="mz_name" value="PepXMLFile_test"/>
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257 <param name="peptideprophet_analyzed" value="false"/>
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258 <param name="score_type" value="qvalue"/>
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259 <section name="fasta_to_mzml">
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260 <param name="isotope_model" value="none"/>
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261 <param name="max_isotope" value="2"/>
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262 <param name="max_isotope_probability" value="0.05"/>
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263 <param name="add_metainfo" value="false"/>
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264 <param name="add_losses" value="false"/>
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265 <param name="sort_by_position" value="true"/>
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266 <param name="add_precursor_peaks" value="false"/>
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267 <param name="add_all_precursor_charges" value="false"/>
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268 <param name="add_abundant_immonium_ions" value="false"/>
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269 <param name="add_first_prefix_ion" value="false"/>
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270 <param name="add_y_ions" value="true"/>
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271 <param name="add_b_ions" value="true"/>
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272 <param name="add_a_ions" value="false"/>
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273 <param name="add_c_ions" value="false"/>
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274 <param name="add_x_ions" value="false"/>
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275 <param name="add_z_ions" value="false"/>
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276 <param name="y_intensity" value="1.0"/>
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277 <param name="b_intensity" value="1.0"/>
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278 <param name="a_intensity" value="1.0"/>
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279 <param name="c_intensity" value="1.0"/>
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280 <param name="x_intensity" value="1.0"/>
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281 <param name="z_intensity" value="1.0"/>
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282 <param name="relative_loss_intensity" value="0.1"/>
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283 <param name="precursor_intensity" value="1.0"/>
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284 <param name="precursor_H2O_intensity" value="1.0"/>
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285 <param name="precursor_NH3_intensity" value="1.0"/>
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286 <param name="enzyme" value="Trypsin"/>
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287 <param name="missed_cleavages" value="0"/>
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288 <param name="min_charge" value="1"/>
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289 <param name="max_charge" value="1"/>
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290 <param name="precursor_charge" value="0"/>
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291 </section>
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292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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293 <output name="ctd_out" ftype="xml">
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294 <assert_contents>
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295 <is_valid_xml/>
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296 </assert_contents>
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297 </output>
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298 </test>
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299 <!-- TOPP_IDFileConverter_3 -->
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300 <test expect_num_outputs="2">
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301 <section name="adv_opts">
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302 <param name="ignore_proteins_per_peptide" value="false"/>
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303 <param name="scan_regex" value=""/>
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304 <param name="no_spectra_data_override" value="false"/>
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305 <param name="no_spectra_references_override" value="false"/>
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306 <param name="add_ionmatch_annotation" value="0.0"/>
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307 <param name="concatenate_peptides" value="false"/>
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308 <param name="number_of_hits" value="1"/>
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309 <param name="force" value="false"/>
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310 <param name="test" value="true"/>
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311 </section>
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312 <param name="in" value="IDFileConverter_3_input.protXML"/>
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313 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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314 <param name="out_type" value="idXML"/>
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315 <param name="mz_name" value=""/>
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316 <param name="peptideprophet_analyzed" value="false"/>
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317 <param name="score_type" value="qvalue"/>
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318 <section name="fasta_to_mzml">
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319 <param name="isotope_model" value="none"/>
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320 <param name="max_isotope" value="2"/>
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321 <param name="max_isotope_probability" value="0.05"/>
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322 <param name="add_metainfo" value="false"/>
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323 <param name="add_losses" value="false"/>
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324 <param name="sort_by_position" value="true"/>
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325 <param name="add_precursor_peaks" value="false"/>
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326 <param name="add_all_precursor_charges" value="false"/>
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327 <param name="add_abundant_immonium_ions" value="false"/>
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328 <param name="add_first_prefix_ion" value="false"/>
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329 <param name="add_y_ions" value="true"/>
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330 <param name="add_b_ions" value="true"/>
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331 <param name="add_a_ions" value="false"/>
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332 <param name="add_c_ions" value="false"/>
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333 <param name="add_x_ions" value="false"/>
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334 <param name="add_z_ions" value="false"/>
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335 <param name="y_intensity" value="1.0"/>
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336 <param name="b_intensity" value="1.0"/>
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337 <param name="a_intensity" value="1.0"/>
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338 <param name="c_intensity" value="1.0"/>
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339 <param name="x_intensity" value="1.0"/>
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340 <param name="z_intensity" value="1.0"/>
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341 <param name="relative_loss_intensity" value="0.1"/>
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342 <param name="precursor_intensity" value="1.0"/>
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343 <param name="precursor_H2O_intensity" value="1.0"/>
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344 <param name="precursor_NH3_intensity" value="1.0"/>
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345 <param name="enzyme" value="Trypsin"/>
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346 <param name="missed_cleavages" value="0"/>
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347 <param name="min_charge" value="1"/>
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348 <param name="max_charge" value="1"/>
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349 <param name="precursor_charge" value="0"/>
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350 </section>
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351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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352 <output name="ctd_out" ftype="xml">
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353 <assert_contents>
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354 <is_valid_xml/>
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355 </assert_contents>
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356 </output>
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357 </test>
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358 <!-- TOPP_IDFileConverter_5 -->
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359 <test expect_num_outputs="2">
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360 <section name="adv_opts">
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361 <param name="ignore_proteins_per_peptide" value="false"/>
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362 <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
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363 <param name="no_spectra_data_override" value="false"/>
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364 <param name="no_spectra_references_override" value="false"/>
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365 <param name="add_ionmatch_annotation" value="0.0"/>
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366 <param name="concatenate_peptides" value="false"/>
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367 <param name="number_of_hits" value="1"/>
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368 <param name="force" value="false"/>
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369 <param name="test" value="true"/>
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370 </section>
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371 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
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372 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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373 <param name="out_type" value="idXML"/>
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374 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
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375 <param name="mz_name" value=""/>
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376 <param name="peptideprophet_analyzed" value="false"/>
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377 <param name="score_type" value="qvalue"/>
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378 <section name="fasta_to_mzml">
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379 <param name="isotope_model" value="none"/>
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380 <param name="max_isotope" value="2"/>
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381 <param name="max_isotope_probability" value="0.05"/>
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382 <param name="add_metainfo" value="false"/>
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383 <param name="add_losses" value="false"/>
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384 <param name="sort_by_position" value="true"/>
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385 <param name="add_precursor_peaks" value="false"/>
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386 <param name="add_all_precursor_charges" value="false"/>
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387 <param name="add_abundant_immonium_ions" value="false"/>
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388 <param name="add_first_prefix_ion" value="false"/>
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389 <param name="add_y_ions" value="true"/>
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390 <param name="add_b_ions" value="true"/>
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391 <param name="add_a_ions" value="false"/>
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392 <param name="add_c_ions" value="false"/>
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393 <param name="add_x_ions" value="false"/>
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394 <param name="add_z_ions" value="false"/>
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395 <param name="y_intensity" value="1.0"/>
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396 <param name="b_intensity" value="1.0"/>
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397 <param name="a_intensity" value="1.0"/>
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398 <param name="c_intensity" value="1.0"/>
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399 <param name="x_intensity" value="1.0"/>
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400 <param name="z_intensity" value="1.0"/>
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401 <param name="relative_loss_intensity" value="0.1"/>
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402 <param name="precursor_intensity" value="1.0"/>
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403 <param name="precursor_H2O_intensity" value="1.0"/>
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404 <param name="precursor_NH3_intensity" value="1.0"/>
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405 <param name="enzyme" value="Trypsin"/>
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406 <param name="missed_cleavages" value="0"/>
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407 <param name="min_charge" value="1"/>
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408 <param name="max_charge" value="1"/>
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409 <param name="precursor_charge" value="0"/>
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410 </section>
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411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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412 <output name="ctd_out" ftype="xml">
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413 <assert_contents>
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414 <is_valid_xml/>
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415 </assert_contents>
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416 </output>
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417 </test>
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418 <!-- TOPP_IDFileConverter_6 -->
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419 <test expect_num_outputs="2">
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420 <section name="adv_opts">
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421 <param name="ignore_proteins_per_peptide" value="false"/>
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422 <param name="scan_regex" value=""/>
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423 <param name="no_spectra_data_override" value="false"/>
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424 <param name="no_spectra_references_override" value="false"/>
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425 <param name="add_ionmatch_annotation" value="0.0"/>
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426 <param name="concatenate_peptides" value="false"/>
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427 <param name="number_of_hits" value="1"/>
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428 <param name="force" value="false"/>
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429 <param name="test" value="true"/>
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430 </section>
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431 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
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432 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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433 <param name="out_type" value="idXML"/>
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434 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
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435 <param name="mz_name" value="F025589.dat.mzML"/>
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436 <param name="peptideprophet_analyzed" value="false"/>
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437 <param name="score_type" value="qvalue"/>
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438 <section name="fasta_to_mzml">
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439 <param name="isotope_model" value="none"/>
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440 <param name="max_isotope" value="2"/>
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441 <param name="max_isotope_probability" value="0.05"/>
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442 <param name="add_metainfo" value="false"/>
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443 <param name="add_losses" value="false"/>
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444 <param name="sort_by_position" value="true"/>
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445 <param name="add_precursor_peaks" value="false"/>
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446 <param name="add_all_precursor_charges" value="false"/>
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447 <param name="add_abundant_immonium_ions" value="false"/>
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448 <param name="add_first_prefix_ion" value="false"/>
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449 <param name="add_y_ions" value="true"/>
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450 <param name="add_b_ions" value="true"/>
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451 <param name="add_a_ions" value="false"/>
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452 <param name="add_c_ions" value="false"/>
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453 <param name="add_x_ions" value="false"/>
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454 <param name="add_z_ions" value="false"/>
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455 <param name="y_intensity" value="1.0"/>
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456 <param name="b_intensity" value="1.0"/>
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457 <param name="a_intensity" value="1.0"/>
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458 <param name="c_intensity" value="1.0"/>
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459 <param name="x_intensity" value="1.0"/>
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460 <param name="z_intensity" value="1.0"/>
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461 <param name="relative_loss_intensity" value="0.1"/>
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462 <param name="precursor_intensity" value="1.0"/>
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463 <param name="precursor_H2O_intensity" value="1.0"/>
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464 <param name="precursor_NH3_intensity" value="1.0"/>
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465 <param name="enzyme" value="Trypsin"/>
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466 <param name="missed_cleavages" value="0"/>
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467 <param name="min_charge" value="1"/>
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468 <param name="max_charge" value="1"/>
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469 <param name="precursor_charge" value="0"/>
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470 </section>
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471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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472 <output name="ctd_out" ftype="xml">
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473 <assert_contents>
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474 <is_valid_xml/>
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475 </assert_contents>
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476 </output>
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477 </test>
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478 <!-- TOPP_IDFileConverter_7 -->
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479 <test expect_num_outputs="2">
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480 <section name="adv_opts">
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481 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
482 <param name="scan_regex" value=""/>
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483 <param name="no_spectra_data_override" value="false"/>
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484 <param name="no_spectra_references_override" value="false"/>
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485 <param name="add_ionmatch_annotation" value="0.0"/>
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486 <param name="concatenate_peptides" value="false"/>
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487 <param name="number_of_hits" value="1"/>
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488 <param name="force" value="false"/>
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489 <param name="test" value="true"/>
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490 </section>
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491 <param name="in" value="IDFileConverter_7_input1.xml"/>
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492 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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493 <param name="out_type" value="idXML"/>
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494 <param name="mz_name" value=""/>
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495 <param name="peptideprophet_analyzed" value="false"/>
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496 <param name="score_type" value="qvalue"/>
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497 <section name="fasta_to_mzml">
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498 <param name="isotope_model" value="none"/>
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499 <param name="max_isotope" value="2"/>
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500 <param name="max_isotope_probability" value="0.05"/>
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501 <param name="add_metainfo" value="false"/>
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502 <param name="add_losses" value="false"/>
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503 <param name="sort_by_position" value="true"/>
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504 <param name="add_precursor_peaks" value="false"/>
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505 <param name="add_all_precursor_charges" value="false"/>
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506 <param name="add_abundant_immonium_ions" value="false"/>
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507 <param name="add_first_prefix_ion" value="false"/>
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508 <param name="add_y_ions" value="true"/>
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509 <param name="add_b_ions" value="true"/>
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510 <param name="add_a_ions" value="false"/>
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diff changeset
511 <param name="add_c_ions" value="false"/>
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512 <param name="add_x_ions" value="false"/>
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diff changeset
513 <param name="add_z_ions" value="false"/>
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diff changeset
514 <param name="y_intensity" value="1.0"/>
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515 <param name="b_intensity" value="1.0"/>
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516 <param name="a_intensity" value="1.0"/>
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diff changeset
517 <param name="c_intensity" value="1.0"/>
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diff changeset
518 <param name="x_intensity" value="1.0"/>
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519 <param name="z_intensity" value="1.0"/>
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diff changeset
520 <param name="relative_loss_intensity" value="0.1"/>
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diff changeset
521 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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522 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
523 <param name="precursor_NH3_intensity" value="1.0"/>
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diff changeset
524 <param name="enzyme" value="Trypsin"/>
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diff changeset
525 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
526 <param name="min_charge" value="1"/>
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diff changeset
527 <param name="max_charge" value="1"/>
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528 <param name="precursor_charge" value="0"/>
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diff changeset
529 </section>
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530 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
531 <output name="ctd_out" ftype="xml">
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532 <assert_contents>
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533 <is_valid_xml/>
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534 </assert_contents>
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diff changeset
535 </output>
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diff changeset
536 </test>
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diff changeset
537 <!-- TOPP_IDFileConverter_8 -->
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diff changeset
538 <test expect_num_outputs="2">
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diff changeset
539 <section name="adv_opts">
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diff changeset
540 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
541 <param name="scan_regex" value=""/>
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diff changeset
542 <param name="no_spectra_data_override" value="false"/>
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diff changeset
543 <param name="no_spectra_references_override" value="false"/>
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diff changeset
544 <param name="add_ionmatch_annotation" value="0.0"/>
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diff changeset
545 <param name="concatenate_peptides" value="false"/>
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diff changeset
546 <param name="number_of_hits" value="1"/>
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diff changeset
547 <param name="force" value="false"/>
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diff changeset
548 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
549 </section>
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diff changeset
550 <param name="in" value="IDFileConverter_8_input.mzid"/>
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551 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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diff changeset
552 <param name="out_type" value="idXML"/>
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553 <param name="mz_name" value=""/>
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diff changeset
554 <param name="peptideprophet_analyzed" value="false"/>
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diff changeset
555 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
556 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
557 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
558 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
559 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
560 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
561 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
562 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
563 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
564 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
565 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
566 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
567 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
568 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
569 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
570 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
571 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
572 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
573 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
574 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
575 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
576 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
577 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
578 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
579 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
580 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
581 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
582 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
583 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
584 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
585 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
586 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
587 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
588 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
589 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
590 <output name="ctd_out" ftype="xml">
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galaxyp
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diff changeset
591 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
592 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
593 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
594 </output>
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galaxyp
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diff changeset
595 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
596 <!-- TOPP_IDFileConverter_9 -->
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galaxyp
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diff changeset
597 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
598 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
599 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
600 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
601 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
602 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
603 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
604 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
605 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
606 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
607 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
608 </section>
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galaxyp
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diff changeset
609 <param name="in" value="IDFileConverter_9_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
610 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
611 <param name="out_type" value="mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
612 <param name="mz_name" value=""/>
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galaxyp
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diff changeset
613 <param name="peptideprophet_analyzed" value="false"/>
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diff changeset
614 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
615 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
616 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
617 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
618 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
619 <param name="add_metainfo" value="false"/>
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diff changeset
620 <param name="add_losses" value="false"/>
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galaxyp
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diff changeset
621 <param name="sort_by_position" value="true"/>
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diff changeset
622 <param name="add_precursor_peaks" value="false"/>
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diff changeset
623 <param name="add_all_precursor_charges" value="false"/>
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diff changeset
624 <param name="add_abundant_immonium_ions" value="false"/>
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diff changeset
625 <param name="add_first_prefix_ion" value="false"/>
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diff changeset
626 <param name="add_y_ions" value="true"/>
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diff changeset
627 <param name="add_b_ions" value="true"/>
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diff changeset
628 <param name="add_a_ions" value="false"/>
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diff changeset
629 <param name="add_c_ions" value="false"/>
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diff changeset
630 <param name="add_x_ions" value="false"/>
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diff changeset
631 <param name="add_z_ions" value="false"/>
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galaxyp
parents: 13
diff changeset
632 <param name="y_intensity" value="1.0"/>
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diff changeset
633 <param name="b_intensity" value="1.0"/>
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diff changeset
634 <param name="a_intensity" value="1.0"/>
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diff changeset
635 <param name="c_intensity" value="1.0"/>
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diff changeset
636 <param name="x_intensity" value="1.0"/>
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diff changeset
637 <param name="z_intensity" value="1.0"/>
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diff changeset
638 <param name="relative_loss_intensity" value="0.1"/>
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639 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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640 <param name="precursor_H2O_intensity" value="1.0"/>
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galaxyp
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641 <param name="precursor_NH3_intensity" value="1.0"/>
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galaxyp
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642 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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643 <param name="missed_cleavages" value="0"/>
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galaxyp
parents: 13
diff changeset
644 <param name="min_charge" value="1"/>
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galaxyp
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645 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
646 <param name="precursor_charge" value="0"/>
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galaxyp
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diff changeset
647 </section>
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648 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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649 <output name="ctd_out" ftype="xml">
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650 <assert_contents>
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galaxyp
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diff changeset
651 <is_valid_xml/>
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diff changeset
652 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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653 </output>
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diff changeset
654 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
655 <!-- TOPP_IDFileConverter_10 -->
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diff changeset
656 <test expect_num_outputs="2">
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657 <section name="adv_opts">
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galaxyp
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diff changeset
658 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
659 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
660 <param name="no_spectra_data_override" value="false"/>
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diff changeset
661 <param name="no_spectra_references_override" value="false"/>
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diff changeset
662 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
663 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
664 <param name="number_of_hits" value="1"/>
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diff changeset
665 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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666 <param name="test" value="true"/>
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diff changeset
667 </section>
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diff changeset
668 <param name="in" value="IDFileConverter_10_input.pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
669 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
670 <param name="out_type" value="idXML"/>
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671 <param name="mz_name" value=""/>
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672 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
673 <param name="score_type" value="qvalue"/>
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diff changeset
674 <section name="fasta_to_mzml">
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675 <param name="isotope_model" value="none"/>
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diff changeset
676 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
677 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
678 <param name="add_metainfo" value="false"/>
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diff changeset
679 <param name="add_losses" value="false"/>
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diff changeset
680 <param name="sort_by_position" value="true"/>
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681 <param name="add_precursor_peaks" value="false"/>
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diff changeset
682 <param name="add_all_precursor_charges" value="false"/>
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diff changeset
683 <param name="add_abundant_immonium_ions" value="false"/>
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684 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
685 <param name="add_y_ions" value="true"/>
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diff changeset
686 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
687 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
688 <param name="add_c_ions" value="false"/>
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diff changeset
689 <param name="add_x_ions" value="false"/>
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diff changeset
690 <param name="add_z_ions" value="false"/>
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diff changeset
691 <param name="y_intensity" value="1.0"/>
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diff changeset
692 <param name="b_intensity" value="1.0"/>
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diff changeset
693 <param name="a_intensity" value="1.0"/>
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diff changeset
694 <param name="c_intensity" value="1.0"/>
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diff changeset
695 <param name="x_intensity" value="1.0"/>
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diff changeset
696 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
697 <param name="relative_loss_intensity" value="0.1"/>
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diff changeset
698 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
699 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
700 <param name="precursor_NH3_intensity" value="1.0"/>
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diff changeset
701 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
702 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
703 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
704 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
705 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
706 </section>
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diff changeset
707 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
708 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
709 <assert_contents>
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diff changeset
710 <is_valid_xml/>
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galaxyp
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diff changeset
711 </assert_contents>
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diff changeset
712 </output>
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diff changeset
713 </test>
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diff changeset
714 <!-- TOPP_IDFileConverter_11 -->
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galaxyp
parents: 13
diff changeset
715 <test expect_num_outputs="2">
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diff changeset
716 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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717 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
718 <param name="scan_regex" value=""/>
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diff changeset
719 <param name="no_spectra_data_override" value="false"/>
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diff changeset
720 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
721 <param name="add_ionmatch_annotation" value="0.0"/>
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diff changeset
722 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
723 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
724 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
725 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
726 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
727 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
728 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
729 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
730 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
731 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
732 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
733 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
734 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
735 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
736 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
737 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
738 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
739 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
740 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
741 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
742 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
743 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
744 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
745 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
746 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
747 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
748 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
749 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
750 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
751 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
752 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
753 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
754 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
755 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
756 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
757 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
758 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
759 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
760 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
761 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
762 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
763 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
764 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
765 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
766 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
767 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
768 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
769 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
770 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
771 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
772 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
773 <!-- TOPP_IDFileConverter_12 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
774 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
775 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
776 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
777 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
778 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
779 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
780 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
781 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
782 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
783 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
784 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
785 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
786 <param name="in" value="IDFileConverter_12_input.psms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
787 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
788 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
789 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
790 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
791 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
792 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
793 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
794 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
795 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
796 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
797 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
798 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
799 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
800 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
801 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
802 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
803 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
804 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
805 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
806 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
807 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
808 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
809 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
810 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
811 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
812 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
813 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
814 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
815 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
816 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
817 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
818 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
819 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
820 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
821 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
822 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
823 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
824 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
826 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
827 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
828 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
829 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
830 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
831 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
832 <!-- TOPP_IDFileConverter_13 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
833 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
834 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
835 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
836 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
837 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
838 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
839 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
840 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
841 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
842 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
843 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
844 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
845 <param name="in" value="IDFileConverter_12_input.psms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
846 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
847 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
848 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
849 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
850 <param name="score_type" value="PEP"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
851 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
852 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
853 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
854 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
855 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
856 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
857 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
858 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
859 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
860 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
861 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
862 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
863 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
864 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
865 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
866 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
867 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
868 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
869 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
870 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
871 <param name="c_intensity" value="1.0"/>
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galaxyp
parents: 13
diff changeset
872 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
873 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
874 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
875 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
876 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
877 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
878 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
879 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
880 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
881 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
882 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
883 </section>
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parents: 13
diff changeset
884 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
885 <output name="ctd_out" ftype="xml">
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galaxyp
parents: 13
diff changeset
886 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
887 <is_valid_xml/>
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diff changeset
888 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
889 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
890 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
891 <!-- TOPP_IDFileConverter_14 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
892 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
893 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
894 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
895 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
896 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
897 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
898 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
899 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
900 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
901 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
902 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
903 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
904 <param name="in" value="IDFileConverter_12_input.psms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
905 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
906 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
907 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
908 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
909 <param name="score_type" value="score"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
910 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
911 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
912 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
913 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
914 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
915 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
916 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
917 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
918 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
919 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
920 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
921 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
922 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
923 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
924 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
925 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
926 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
927 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
928 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
929 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
930 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
931 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
932 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
933 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
934 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
935 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
936 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
937 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
938 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
939 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
940 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
941 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
942 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
944 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
945 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
946 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
947 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
948 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
949 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
950 <!-- TOPP_IDFileConverter_15 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
951 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
952 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
953 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
954 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
955 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
956 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
957 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
958 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
959 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
960 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
961 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
962 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
963 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
964 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
965 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
966 <param name="mz_file" value="spectra.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
967 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
968 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
969 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
970 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
971 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
972 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
973 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
974 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
975 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
976 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
977 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
978 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
979 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
980 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
981 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
982 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
983 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
984 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
985 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
986 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
987 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
988 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
989 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
990 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
991 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
992 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
993 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
994 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
995 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
996 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
997 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
998 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
999 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1000 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1001 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1002 </section>
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galaxyp
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diff changeset
1003 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1004 <output name="ctd_out" ftype="xml">
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diff changeset
1005 <assert_contents>
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galaxyp
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diff changeset
1006 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1007 </assert_contents>
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galaxyp
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diff changeset
1008 </output>
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galaxyp
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diff changeset
1009 </test>
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galaxyp
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diff changeset
1010 <!-- TOPP_IDFileConverter_16 -->
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galaxyp
parents: 13
diff changeset
1011 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1012 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1013 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1014 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1015 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1016 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1017 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1018 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1019 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1020 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1021 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1022 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1023 <param name="in" value="IDFileConverter_16_input.pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1024 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1025 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1026 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1027 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1028 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1029 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1030 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1031 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1032 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1033 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1034 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1035 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1036 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1037 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1038 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1039 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1040 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1041 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1042 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1043 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1044 <param name="add_x_ions" value="false"/>
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parents: 13
diff changeset
1045 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1046 <param name="y_intensity" value="1.0"/>
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parents: 13
diff changeset
1047 <param name="b_intensity" value="1.0"/>
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diff changeset
1048 <param name="a_intensity" value="1.0"/>
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diff changeset
1049 <param name="c_intensity" value="1.0"/>
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diff changeset
1050 <param name="x_intensity" value="1.0"/>
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diff changeset
1051 <param name="z_intensity" value="1.0"/>
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diff changeset
1052 <param name="relative_loss_intensity" value="0.1"/>
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diff changeset
1053 <param name="precursor_intensity" value="1.0"/>
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parents: 13
diff changeset
1054 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1055 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1056 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1057 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1058 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1059 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1060 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1061 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1062 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1063 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1064 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1065 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1066 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1067 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1068 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1069 <!-- TOPP_IDFileConverter_17 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1070 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1071 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1072 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1073 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1074 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1075 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1076 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1077 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1078 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1079 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1080 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1081 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1082 <param name="in" value="IDFileConverter_17_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1083 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1084 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1085 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1086 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1087 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1088 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1089 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1090 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1091 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1092 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1093 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1094 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1095 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1096 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1097 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1098 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1099 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1100 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1101 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1102 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1103 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1104 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1105 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1106 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1107 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1108 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1109 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1110 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1111 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1112 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1113 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1114 <param name="precursor_NH3_intensity" value="1.0"/>
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diff changeset
1115 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1116 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1117 <param name="min_charge" value="1"/>
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diff changeset
1118 <param name="max_charge" value="1"/>
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diff changeset
1119 <param name="precursor_charge" value="0"/>
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diff changeset
1120 </section>
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diff changeset
1121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
1122 <output name="ctd_out" ftype="xml">
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diff changeset
1123 <assert_contents>
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diff changeset
1124 <is_valid_xml/>
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diff changeset
1125 </assert_contents>
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diff changeset
1126 </output>
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diff changeset
1127 </test>
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diff changeset
1128 <!-- TOPP_IDFileConverter_18 -->
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diff changeset
1129 <test expect_num_outputs="2">
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diff changeset
1130 <section name="adv_opts">
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diff changeset
1131 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
1132 <param name="scan_regex" value=""/>
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diff changeset
1133 <param name="no_spectra_data_override" value="false"/>
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diff changeset
1134 <param name="no_spectra_references_override" value="false"/>
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diff changeset
1135 <param name="add_ionmatch_annotation" value="0.0"/>
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diff changeset
1136 <param name="concatenate_peptides" value="false"/>
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diff changeset
1137 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1138 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1139 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1140 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1141 <param name="in" value="IDFileConverter_18_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1142 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1143 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1144 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1145 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1146 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1147 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1148 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1149 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1150 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1151 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1152 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1153 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1154 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1155 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1156 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1157 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1158 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1159 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1160 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1161 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1162 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1163 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1164 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1165 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1166 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1167 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1168 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1169 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1170 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1171 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1172 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1173 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1174 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1175 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1176 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1177 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1178 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1179 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1180 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1181 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1182 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1183 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1184 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1185 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1186 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1187 <!-- TOPP_IDFileConverter_19 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1188 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1189 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1190 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1191 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1192 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1193 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1194 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1195 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1196 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1197 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1198 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1199 </section>
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galaxyp
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diff changeset
1200 <param name="in" value="IDFileConverter_19_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1201 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1202 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1203 <param name="mz_name" value=""/>
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diff changeset
1204 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1205 <param name="score_type" value="qvalue"/>
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diff changeset
1206 <section name="fasta_to_mzml">
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diff changeset
1207 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1208 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1209 <param name="max_isotope_probability" value="0.05"/>
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diff changeset
1210 <param name="add_metainfo" value="false"/>
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diff changeset
1211 <param name="add_losses" value="false"/>
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galaxyp
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diff changeset
1212 <param name="sort_by_position" value="true"/>
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diff changeset
1213 <param name="add_precursor_peaks" value="false"/>
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diff changeset
1214 <param name="add_all_precursor_charges" value="false"/>
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diff changeset
1215 <param name="add_abundant_immonium_ions" value="false"/>
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diff changeset
1216 <param name="add_first_prefix_ion" value="false"/>
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diff changeset
1217 <param name="add_y_ions" value="true"/>
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diff changeset
1218 <param name="add_b_ions" value="true"/>
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diff changeset
1219 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1220 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1221 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1222 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1223 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1224 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1225 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1226 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1227 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1228 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1229 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1230 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1231 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1232 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1233 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1234 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1235 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1236 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1237 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1238 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1240 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1241 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1242 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1243 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1244 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1245 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1246 <!-- TOPP_IDFileConverter_20 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1247 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1248 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1249 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1250 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1251 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1252 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1253 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1254 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1255 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1256 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1257 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1258 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1259 <param name="in" value="IDFileConverter_20_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1260 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1261 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1262 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1263 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1264 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1265 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1266 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1267 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1268 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1269 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1270 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1271 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1272 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1273 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1274 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1275 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1276 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1277 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1278 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1279 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1280 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1281 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1282 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1283 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1284 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1285 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1286 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1287 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1288 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1289 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1290 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
1291 <param name="precursor_NH3_intensity" value="1.0"/>
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diff changeset
1292 <param name="enzyme" value="Trypsin"/>
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diff changeset
1293 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1294 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1295 <param name="max_charge" value="1"/>
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diff changeset
1296 <param name="precursor_charge" value="0"/>
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diff changeset
1297 </section>
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diff changeset
1298 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
1299 <output name="ctd_out" ftype="xml">
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diff changeset
1300 <assert_contents>
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diff changeset
1301 <is_valid_xml/>
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diff changeset
1302 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1303 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1304 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1305 <!-- TOPP_IDFileConverter_21 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1306 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1307 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1308 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1309 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1310 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1311 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1312 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1313 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1314 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1315 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1316 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1317 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1318 <param name="in" value="IDFileConverter_21_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1319 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1320 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1321 <param name="mz_file" value="IDMapper_4_input.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1322 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1323 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1324 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1325 <section name="fasta_to_mzml">
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galaxyp
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diff changeset
1326 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1327 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1328 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1329 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1330 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1331 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1332 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1333 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1334 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1335 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1336 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1337 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1338 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1339 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1340 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1341 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1342 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1343 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1344 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1345 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1346 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1347 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1348 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1349 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1350 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
1351 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1352 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1353 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1354 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1355 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1356 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1357 </section>
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diff changeset
1358 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1359 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1360 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1361 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1362 </assert_contents>
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diff changeset
1363 </output>
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diff changeset
1364 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1365 <!-- TOPP_IDFileConverter_22 -->
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galaxyp
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diff changeset
1366 <test expect_num_outputs="2">
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diff changeset
1367 <section name="adv_opts">
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diff changeset
1368 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
1369 <param name="scan_regex" value=""/>
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diff changeset
1370 <param name="no_spectra_data_override" value="false"/>
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diff changeset
1371 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1372 <param name="add_ionmatch_annotation" value="0.01"/>
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diff changeset
1373 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1374 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1375 <param name="force" value="false"/>
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diff changeset
1376 <param name="test" value="true"/>
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diff changeset
1377 </section>
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diff changeset
1378 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1379 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1380 <param name="out_type" value="idXML"/>
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diff changeset
1381 <param name="mz_file" value="spectra.mzML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1382 <param name="mz_name" value=""/>
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diff changeset
1383 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1384 <param name="score_type" value="qvalue"/>
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parents: 13
diff changeset
1385 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1386 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1387 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1388 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1389 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1390 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1391 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1392 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1393 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1394 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1395 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1396 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1397 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1398 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1399 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1400 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1401 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1402 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1403 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1404 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1405 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1406 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1407 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1408 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1409 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1410 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1411 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1412 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1413 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1414 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1415 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1416 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1417 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1418 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1419 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1420 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1421 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1422 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1423 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1424 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1425 <!-- TOPP_IDFileConverter_23 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1426 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1427 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1428 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1429 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1430 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1431 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1432 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1433 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1434 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1435 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1436 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1437 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1438 <param name="in" value="IDFileConverter_23_input.mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1439 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1440 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1441 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1442 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1443 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1444 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1445 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1446 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1447 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1448 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1449 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1450 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1451 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1452 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1453 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1454 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1455 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1456 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1457 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1458 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1459 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1460 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1461 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1462 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1463 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1464 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1465 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1466 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1467 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1468 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1469 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1470 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1471 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1472 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1473 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1474 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1475 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1476 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1478 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1479 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1480 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1481 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1482 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1483 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1484 <!-- TOPP_IDFileConverter_24 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1485 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1486 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1487 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1488 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1489 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1490 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1491 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1492 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1493 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1494 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1495 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1496 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1497 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1498 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1499 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1500 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1501 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1502 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1503 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1504 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1505 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1506 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1507 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1508 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1509 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1510 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1511 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1512 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1513 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1514 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1515 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1516 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1517 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1518 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1519 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1520 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1521 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1522 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1523 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1524 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1525 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1526 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1527 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1528 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1529 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1530 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1531 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1532 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1533 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1534 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1535 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1536 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1537 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1538 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1539 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1540 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1541 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1542 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1543 <!-- TOPP_IDFileConverter_25 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1544 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1545 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1546 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1547 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1548 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1549 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1550 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1551 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1552 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1553 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1554 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1555 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1556 <param name="in" value="IDFileConverter_25_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1557 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1558 <param name="out_type" value="pepXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1559 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1560 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1561 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1562 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1563 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1564 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1565 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1566 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1567 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1568 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1569 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1570 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1571 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1572 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1573 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1574 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1575 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1576 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1577 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1578 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1579 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1580 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1581 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1582 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1583 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1584 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1585 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1586 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1587 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1588 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1589 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1590 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1591 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1592 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1593 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1594 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1596 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1597 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1598 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1599 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1600 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1601 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1602 <!-- TOPP_IDFileConverter_26 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1603 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1604 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1605 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1606 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1607 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1608 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1609 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1610 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1611 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1612 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1613 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1614 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1615 <param name="in" value="IDFileConverter_26_input.mzid"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1616 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1617 <param name="out_type" value="idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1618 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1619 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1620 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1621 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1622 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1623 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1624 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1625 <param name="add_metainfo" value="false"/>
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galaxyp
parents: 13
diff changeset
1626 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1627 <param name="sort_by_position" value="true"/>
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diff changeset
1628 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1629 <param name="add_all_precursor_charges" value="false"/>
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galaxyp
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diff changeset
1630 <param name="add_abundant_immonium_ions" value="false"/>
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diff changeset
1631 <param name="add_first_prefix_ion" value="false"/>
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diff changeset
1632 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1633 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1634 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1635 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1636 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1637 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1638 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1639 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1640 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1641 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1642 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1643 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1644 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1645 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1646 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1647 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1648 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1649 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1650 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1651 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1652 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1653 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1654 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1655 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1656 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1657 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1658 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1659 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1660 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1661 <!-- TOPP_IDFileConverter_27 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1662 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1663 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1664 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1665 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1666 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1667 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1668 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1669 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1670 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1671 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1672 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1673 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1674 <param name="in" value="IDFileConverter_27_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1675 <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1676 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1677 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1678 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1679 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1680 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1681 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1682 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1683 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1684 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1685 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1686 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1687 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1688 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1689 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1690 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1691 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1692 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1693 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1694 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1695 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1696 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1697 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1698 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1699 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1700 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1701 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1702 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1703 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1704 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1705 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1706 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1707 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1708 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1709 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1710 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1711 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1712 </section>
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galaxyp
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diff changeset
1713 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
1714 <output name="ctd_out" ftype="xml">
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galaxyp
parents: 13
diff changeset
1715 <assert_contents>
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galaxyp
parents: 13
diff changeset
1716 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1717 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1718 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1719 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1720 <!-- TOPP_IDFileConverter_28 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1721 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1722 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1723 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1724 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1725 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1726 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1727 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1728 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1729 <param name="number_of_hits" value="-1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1730 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1731 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1732 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1733 <param name="in" value="IDFileConverter_27_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1734 <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1735 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1736 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1737 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1738 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1739 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1740 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1741 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1742 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1743 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1744 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1745 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1746 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1747 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1748 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1749 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1750 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1751 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1752 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1753 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1754 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1755 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1756 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1757 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1758 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1759 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1760 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1761 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1762 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1763 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1764 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1765 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1766 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1767 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1768 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1769 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1770 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1771 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1773 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1774 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1775 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1776 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1777 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1778 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1779 <!-- TOPP_IDFileConverter_29 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1780 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1781 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1782 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1783 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1784 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1785 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1786 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1787 <param name="concatenate_peptides" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1788 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1789 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1790 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1791 </section>
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galaxyp
parents: 13
diff changeset
1792 <param name="in" value="IDFileConverter_27_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1793 <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1794 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1795 <param name="mz_name" value=""/>
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diff changeset
1796 <param name="peptideprophet_analyzed" value="false"/>
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galaxyp
parents: 13
diff changeset
1797 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1798 <section name="fasta_to_mzml">
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parents: 13
diff changeset
1799 <param name="isotope_model" value="none"/>
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diff changeset
1800 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1801 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1802 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1803 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1804 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1805 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1806 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1807 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1808 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1809 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1810 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1811 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1812 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1813 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1814 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1815 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1816 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1817 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1818 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1819 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1820 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1821 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1822 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1823 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
1824 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1825 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1826 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1827 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1828 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1829 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1830 </section>
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diff changeset
1831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1832 <output name="ctd_out" ftype="xml">
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galaxyp
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diff changeset
1833 <assert_contents>
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galaxyp
parents: 13
diff changeset
1834 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1835 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1836 </output>
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diff changeset
1837 </test>
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parents: 13
diff changeset
1838 <!-- TOPP_IDFileConverter_30 -->
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galaxyp
parents: 13
diff changeset
1839 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1840 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1841 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
1842 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1843 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1844 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1845 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1846 <param name="concatenate_peptides" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1847 <param name="number_of_hits" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1848 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1849 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1850 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1851 <param name="in" value="IDFileConverter_27_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1852 <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1853 <param name="out_type" value="fasta"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1854 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1855 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1856 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1857 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1858 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1859 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1860 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1861 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1862 <param name="add_losses" value="false"/>
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diff changeset
1863 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1864 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1865 <param name="add_all_precursor_charges" value="false"/>
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diff changeset
1866 <param name="add_abundant_immonium_ions" value="false"/>
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diff changeset
1867 <param name="add_first_prefix_ion" value="false"/>
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diff changeset
1868 <param name="add_y_ions" value="true"/>
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diff changeset
1869 <param name="add_b_ions" value="true"/>
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diff changeset
1870 <param name="add_a_ions" value="false"/>
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diff changeset
1871 <param name="add_c_ions" value="false"/>
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diff changeset
1872 <param name="add_x_ions" value="false"/>
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diff changeset
1873 <param name="add_z_ions" value="false"/>
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diff changeset
1874 <param name="y_intensity" value="1.0"/>
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diff changeset
1875 <param name="b_intensity" value="1.0"/>
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diff changeset
1876 <param name="a_intensity" value="1.0"/>
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diff changeset
1877 <param name="c_intensity" value="1.0"/>
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diff changeset
1878 <param name="x_intensity" value="1.0"/>
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diff changeset
1879 <param name="z_intensity" value="1.0"/>
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diff changeset
1880 <param name="relative_loss_intensity" value="0.1"/>
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parents: 13
diff changeset
1881 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1882 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
1883 <param name="precursor_NH3_intensity" value="1.0"/>
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galaxyp
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diff changeset
1884 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1885 <param name="missed_cleavages" value="0"/>
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diff changeset
1886 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1887 <param name="max_charge" value="1"/>
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diff changeset
1888 <param name="precursor_charge" value="0"/>
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diff changeset
1889 </section>
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diff changeset
1890 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
1891 <output name="ctd_out" ftype="xml">
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diff changeset
1892 <assert_contents>
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diff changeset
1893 <is_valid_xml/>
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diff changeset
1894 </assert_contents>
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diff changeset
1895 </output>
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diff changeset
1896 </test>
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diff changeset
1897 <!-- TOPP_IDFileConverter_31 -->
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diff changeset
1898 <test expect_num_outputs="2">
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diff changeset
1899 <section name="adv_opts">
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diff changeset
1900 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
1901 <param name="scan_regex" value=""/>
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diff changeset
1902 <param name="no_spectra_data_override" value="false"/>
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diff changeset
1903 <param name="no_spectra_references_override" value="false"/>
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diff changeset
1904 <param name="add_ionmatch_annotation" value="0.0"/>
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diff changeset
1905 <param name="concatenate_peptides" value="false"/>
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diff changeset
1906 <param name="number_of_hits" value="1"/>
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diff changeset
1907 <param name="force" value="false"/>
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diff changeset
1908 <param name="test" value="true"/>
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diff changeset
1909 </section>
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diff changeset
1910 <param name="in" value="IDFileConverter_31_input.mzid"/>
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diff changeset
1911 <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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diff changeset
1912 <param name="out_type" value="idXML"/>
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diff changeset
1913 <param name="mz_name" value=""/>
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diff changeset
1914 <param name="peptideprophet_analyzed" value="false"/>
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diff changeset
1915 <param name="score_type" value="qvalue"/>
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diff changeset
1916 <section name="fasta_to_mzml">
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diff changeset
1917 <param name="isotope_model" value="none"/>
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diff changeset
1918 <param name="max_isotope" value="2"/>
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diff changeset
1919 <param name="max_isotope_probability" value="0.05"/>
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diff changeset
1920 <param name="add_metainfo" value="false"/>
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diff changeset
1921 <param name="add_losses" value="false"/>
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diff changeset
1922 <param name="sort_by_position" value="true"/>
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diff changeset
1923 <param name="add_precursor_peaks" value="false"/>
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diff changeset
1924 <param name="add_all_precursor_charges" value="false"/>
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diff changeset
1925 <param name="add_abundant_immonium_ions" value="false"/>
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diff changeset
1926 <param name="add_first_prefix_ion" value="false"/>
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diff changeset
1927 <param name="add_y_ions" value="true"/>
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diff changeset
1928 <param name="add_b_ions" value="true"/>
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diff changeset
1929 <param name="add_a_ions" value="false"/>
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1930 <param name="add_c_ions" value="false"/>
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diff changeset
1931 <param name="add_x_ions" value="false"/>
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diff changeset
1932 <param name="add_z_ions" value="false"/>
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1933 <param name="y_intensity" value="1.0"/>
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diff changeset
1934 <param name="b_intensity" value="1.0"/>
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diff changeset
1935 <param name="a_intensity" value="1.0"/>
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diff changeset
1936 <param name="c_intensity" value="1.0"/>
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diff changeset
1937 <param name="x_intensity" value="1.0"/>
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1938 <param name="z_intensity" value="1.0"/>
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diff changeset
1939 <param name="relative_loss_intensity" value="0.1"/>
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diff changeset
1940 <param name="precursor_intensity" value="1.0"/>
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diff changeset
1941 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
1942 <param name="precursor_NH3_intensity" value="1.0"/>
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diff changeset
1943 <param name="enzyme" value="Trypsin"/>
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1944 <param name="missed_cleavages" value="0"/>
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diff changeset
1945 <param name="min_charge" value="1"/>
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diff changeset
1946 <param name="max_charge" value="1"/>
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1947 <param name="precursor_charge" value="0"/>
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diff changeset
1948 </section>
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1949 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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1950 <output name="ctd_out" ftype="xml">
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1951 <assert_contents>
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1952 <is_valid_xml/>
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1953 </assert_contents>
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1954 </output>
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1955 </test>
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1956 <!-- TOPP_IDFileConverter_32 -->
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1957 <test expect_num_outputs="2">
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1958 <section name="adv_opts">
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1959 <param name="ignore_proteins_per_peptide" value="false"/>
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diff changeset
1960 <param name="scan_regex" value=""/>
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1961 <param name="no_spectra_data_override" value="false"/>
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1962 <param name="no_spectra_references_override" value="false"/>
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1963 <param name="add_ionmatch_annotation" value="0.0"/>
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1964 <param name="concatenate_peptides" value="false"/>
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1965 <param name="number_of_hits" value="1"/>
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1966 <param name="force" value="false"/>
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1967 <param name="test" value="true"/>
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1968 </section>
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1969 <param name="in" value="IDFileConverter_32_input.FASTA"/>
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1970 <output name="out" file="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
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1971 <param name="out_type" value="mzML"/>
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1972 <param name="mz_name" value=""/>
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1973 <param name="peptideprophet_analyzed" value="false"/>
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1974 <param name="score_type" value="qvalue"/>
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1975 <section name="fasta_to_mzml">
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1976 <param name="isotope_model" value="none"/>
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1977 <param name="max_isotope" value="2"/>
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1978 <param name="max_isotope_probability" value="0.05"/>
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1979 <param name="add_metainfo" value="false"/>
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1980 <param name="add_losses" value="false"/>
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1981 <param name="sort_by_position" value="true"/>
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1982 <param name="add_precursor_peaks" value="false"/>
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1983 <param name="add_all_precursor_charges" value="false"/>
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1984 <param name="add_abundant_immonium_ions" value="false"/>
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1985 <param name="add_first_prefix_ion" value="false"/>
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1986 <param name="add_y_ions" value="true"/>
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1987 <param name="add_b_ions" value="true"/>
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1988 <param name="add_a_ions" value="false"/>
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1989 <param name="add_c_ions" value="false"/>
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1990 <param name="add_x_ions" value="false"/>
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1991 <param name="add_z_ions" value="false"/>
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1992 <param name="y_intensity" value="1.0"/>
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1993 <param name="b_intensity" value="1.0"/>
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1994 <param name="a_intensity" value="1.0"/>
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1995 <param name="c_intensity" value="1.0"/>
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1996 <param name="x_intensity" value="1.0"/>
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1997 <param name="z_intensity" value="1.0"/>
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1998 <param name="relative_loss_intensity" value="0.1"/>
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1999 <param name="precursor_intensity" value="1.0"/>
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2000 <param name="precursor_H2O_intensity" value="1.0"/>
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2001 <param name="precursor_NH3_intensity" value="1.0"/>
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2002 <param name="enzyme" value="Trypsin"/>
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2003 <param name="missed_cleavages" value="0"/>
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2004 <param name="min_charge" value="1"/>
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2005 <param name="max_charge" value="1"/>
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2006 <param name="precursor_charge" value="0"/>
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diff changeset
2007 </section>
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2008 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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2009 <output name="ctd_out" ftype="xml">
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2010 <assert_contents>
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2011 <is_valid_xml/>
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2012 </assert_contents>
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2013 </output>
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2014 </test>
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2015 <!-- TOPP_IDFileConverter_33 -->
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2016 <test expect_num_outputs="2">
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2017 <section name="adv_opts">
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2018 <param name="ignore_proteins_per_peptide" value="false"/>
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2019 <param name="scan_regex" value=""/>
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2020 <param name="no_spectra_data_override" value="false"/>
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2021 <param name="no_spectra_references_override" value="false"/>
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2022 <param name="add_ionmatch_annotation" value="0.0"/>
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2023 <param name="concatenate_peptides" value="false"/>
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2024 <param name="number_of_hits" value="1"/>
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diff changeset
2025 <param name="force" value="false"/>
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2026 <param name="test" value="true"/>
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diff changeset
2027 </section>
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2028 <param name="in" value="IDFileConverter_32_input.FASTA"/>
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2029 <output name="out" file="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
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2030 <param name="out_type" value="mzML"/>
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2031 <param name="mz_name" value=""/>
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2032 <param name="peptideprophet_analyzed" value="false"/>
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2033 <param name="score_type" value="qvalue"/>
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2034 <section name="fasta_to_mzml">
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2035 <param name="isotope_model" value="none"/>
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2036 <param name="max_isotope" value="2"/>
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2037 <param name="max_isotope_probability" value="0.05"/>
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2038 <param name="add_metainfo" value="false"/>
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2039 <param name="add_losses" value="false"/>
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2040 <param name="sort_by_position" value="true"/>
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2041 <param name="add_precursor_peaks" value="false"/>
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2042 <param name="add_all_precursor_charges" value="false"/>
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2043 <param name="add_abundant_immonium_ions" value="false"/>
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2044 <param name="add_first_prefix_ion" value="false"/>
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2045 <param name="add_y_ions" value="true"/>
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diff changeset
2046 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2047 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2048 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2049 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2050 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2051 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2052 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2053 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2054 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2055 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2056 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2057 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2058 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2059 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2060 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2061 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2062 <param name="missed_cleavages" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2063 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2064 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2065 <param name="precursor_charge" value="3"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2066 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2067 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2068 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2069 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2070 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2071 </assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2072 </output>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2073 </test>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2074 <!-- TOPP_IDFileConverter_34_1 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2075 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2076 <section name="adv_opts">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2077 <param name="ignore_proteins_per_peptide" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2078 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2079 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2080 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2081 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2082 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2083 <param name="number_of_hits" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2084 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2085 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2086 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2087 <param name="in" value="IDFileConverter_34_input.idXML"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2088 <output name="out" file="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2089 <param name="out_type" value="oms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2090 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2091 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2092 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2093 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2094 <param name="isotope_model" value="none"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2095 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2096 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2097 <param name="add_metainfo" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2098 <param name="add_losses" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2099 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2100 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2101 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2102 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2103 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2104 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2105 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2106 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2107 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2108 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2109 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2110 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2111 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2112 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2113 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2114 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2115 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2116 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2117 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2118 <param name="precursor_H2O_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2119 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2120 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2121 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2122 <param name="min_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2123 <param name="max_charge" value="1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2124 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2125 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2126 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2127 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2128 <assert_contents>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2129 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2130 </assert_contents>
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diff changeset
2131 </output>
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diff changeset
2132 </test>
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galaxyp
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diff changeset
2133 <!-- TOPP_IDFileConverter_34_2 -->
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2134 <test expect_num_outputs="2">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2135 <section name="adv_opts">
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diff changeset
2136 <param name="ignore_proteins_per_peptide" value="false"/>
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galaxyp
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diff changeset
2137 <param name="scan_regex" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2138 <param name="no_spectra_data_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2139 <param name="no_spectra_references_override" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
2140 <param name="add_ionmatch_annotation" value="0.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2141 <param name="concatenate_peptides" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2142 <param name="number_of_hits" value="1"/>
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galaxyp
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diff changeset
2143 <param name="force" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2144 <param name="test" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2145 </section>
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galaxyp
parents: 13
diff changeset
2146 <param name="in" value="IDFileConverter_34_output1.oms"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2147 <output name="out" file="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2148 <param name="out_type" value="idXML"/>
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galaxyp
parents: 13
diff changeset
2149 <param name="mz_name" value=""/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2150 <param name="peptideprophet_analyzed" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2151 <param name="score_type" value="qvalue"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2152 <section name="fasta_to_mzml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
2153 <param name="isotope_model" value="none"/>
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galaxyp
parents: 13
diff changeset
2154 <param name="max_isotope" value="2"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2155 <param name="max_isotope_probability" value="0.05"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2156 <param name="add_metainfo" value="false"/>
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galaxyp
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diff changeset
2157 <param name="add_losses" value="false"/>
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galaxyp
parents: 13
diff changeset
2158 <param name="sort_by_position" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2159 <param name="add_precursor_peaks" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2160 <param name="add_all_precursor_charges" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2161 <param name="add_abundant_immonium_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2162 <param name="add_first_prefix_ion" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2163 <param name="add_y_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2164 <param name="add_b_ions" value="true"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2165 <param name="add_a_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2166 <param name="add_c_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2167 <param name="add_x_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
2168 <param name="add_z_ions" value="false"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
2169 <param name="y_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2170 <param name="b_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2171 <param name="a_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
2172 <param name="c_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2173 <param name="x_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2174 <param name="z_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2175 <param name="relative_loss_intensity" value="0.1"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2176 <param name="precursor_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2177 <param name="precursor_H2O_intensity" value="1.0"/>
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diff changeset
2178 <param name="precursor_NH3_intensity" value="1.0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2179 <param name="enzyme" value="Trypsin"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2180 <param name="missed_cleavages" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2181 <param name="min_charge" value="1"/>
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diff changeset
2182 <param name="max_charge" value="1"/>
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diff changeset
2183 <param name="precursor_charge" value="0"/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2184 </section>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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diff changeset
2186 <output name="ctd_out" ftype="xml">
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2187 <assert_contents>
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diff changeset
2188 <is_valid_xml/>
7d0eb300f360 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
2189 </assert_contents>
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diff changeset
2190 </output>
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diff changeset
2191 </test>
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diff changeset
2192 </tests>
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diff changeset
2193 <help><![CDATA[Converts identification engine file formats.
0
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diff changeset
2194
bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
2195
15
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diff changeset
2196 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFileConverter.html]]></help>
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diff changeset
2197 <expand macro="references"/>
0
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diff changeset
2198 </tool>