Mercurial > repos > galaxyp > openms_cruxadapter

annotate CruxAdapter.xml @ 4:a915cadc2f07 draft default tip

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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 19:08:43 +0000
parents aed7aeb6feec
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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: [Identification]-->
4
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4 <tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Identifies MS/MS spectra using Crux.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CruxAdapter</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($in.ext)' &&
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19 mkdir out &&
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20 mkdir database &&
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21 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("idxml")}'
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33 -database
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34 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
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35
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36 ## Postprocessing
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37 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
4
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46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
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47 <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
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48 <param argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help="">
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49 <expand macro="list_string_san" name="extra_index_args"/>
0
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50 </param>
4
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51 <param argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help="">
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52 <expand macro="list_string_san" name="extra_search_args"/>
0
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53 </param>
4
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54 <param argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help="">
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55 <expand macro="list_string_san" name="extra_percolator_args"/>
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56 </param>
4
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57 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/>
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58 <param argument="-precursor_mass_units" type="select" optional="true" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help="">
0
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59 <option value="mass">mass</option>
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60 <option value="mz">mz</option>
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61 <option value="ppm" selected="true">ppm</option>
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62 <expand macro="list_string_san" name="precursor_mass_units"/>
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63 </param>
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64 <param argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/>
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65 <param argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/>
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66 <param argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help="">
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67 <expand macro="list_string_san" name="isotope_error"/>
0
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68 </param>
4
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69 <param argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
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70 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
0
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71 <option value="custom-enzyme">custom-enzyme</option>
4
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72 <option value="pepsin-a">pepsin-a</option>
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73 <option value="cyanogen-bromide">cyanogen-bromide</option>
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74 <option value="clostripain">clostripain</option>
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75 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
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76 <option value="no-enzyme">no-enzyme</option>
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77 <option value="arg-c">arg-c</option>
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78 <option value="asp-n">asp-n</option>
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parents: 0
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79 <option value="iodosobenzoate">iodosobenzoate</option>
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parents: 0
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80 <option value="staph-protease">staph-protease</option>
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parents: 0
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81 <option value="proline-endopeptidase">proline-endopeptidase</option>
0
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82 <option value="glu-c">glu-c</option>
4
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83 <option value="elastase">elastase</option>
2
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parents: 0
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84 <option value="chymotrypsin">chymotrypsin</option>
0
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85 <option value="lys-c">lys-c</option>
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86 <option value="lys-n">lys-n</option>
4
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87 <option value="trypsin/p">trypsin/p</option>
0
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88 <option value="trypsin" selected="true">trypsin</option>
4
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89 <expand macro="list_string_san" name="enzyme"/>
0
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90 </param>
4
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91 <param argument="-digestion" type="select" optional="true" label="Full, partial or non specific digestion" help="">
0
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92 <option value="full-digest" selected="true">full-digest</option>
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93 <option value="partial-digest">partial-digest</option>
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94 <option value="non-specific-digest">non-specific-digest</option>
4
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95 <expand macro="list_string_san" name="digestion"/>
0
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96 </param>
4
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97 <param argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
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98 <param argument="-decoy_format" type="select" optional="true" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
0
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99 <option value="none">none</option>
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100 <option value="shuffle" selected="true">shuffle</option>
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101 <option value="peptide-reverse">peptide-reverse</option>
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102 <option value="protein-reverse">protein-reverse</option>
4
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103 <expand macro="list_string_san" name="decoy_format"/>
0
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104 </param>
4
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105 <param argument="-keep_terminal_aminos" type="select" optional="true" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
0
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106 <option value="N">N</option>
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107 <option value="C">C</option>
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108 <option value="NC" selected="true">NC</option>
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109 <option value="none">none</option>
4
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110 <expand macro="list_string_san" name="keep_terminal_aminos"/>
0
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111 </param>
4
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112 <param argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;">
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113 <expand macro="list_string_san" name="cterm_modifications"/>
0
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114 </param>
4
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115 <param argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;">
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116 <expand macro="list_string_san" name="nterm_modifications"/>
0
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117 </param>
4
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118 <param argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146">
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119 <expand macro="list_string_san" name="modifications"/>
0
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120 </param>
4
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121 <param argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/>
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122 <param argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/>
0
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123 <expand macro="adv_opts_macro">
4
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124 <param argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. ">
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125 <expand macro="list_string_san" name="custom_enzyme"/>
0
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126 </param>
4
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127 <param argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
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128 <expand macro="list_string_san" name="decoy_prefix"/>
0
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129 </param>
4
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130 <param argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
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131 <param argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
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132 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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133 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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134 <expand macro="list_string_san" name="test"/>
0
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135 </param>
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136 </expand>
2
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137 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
0
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138 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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139 </param>
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140 </inputs>
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141 <outputs>
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142 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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143 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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144 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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145 </data>
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146 </outputs>
4
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147 <tests><!-- TOPP_CruxAdapter_1 -->
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148 <test expect_num_outputs="2">
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149 <section name="adv_opts">
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150 <param name="custom_enzyme" value=""/>
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151 <param name="decoy_prefix" value="decoy_"/>
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152 <param name="deisotope" value="false"/>
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153 <param name="report_decoys" value="false"/>
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154 <param name="force" value="false"/>
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155 <param name="test" value="true"/>
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156 </section>
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157 <param name="in" value="spectra_comet.mzML"/>
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158 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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159 <param name="database" value="proteins.fasta"/>
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160 <param name="extra_index_args" value=""/>
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161 <param name="extra_search_args" value=""/>
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162 <param name="extra_percolator_args" value=""/>
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163 <param name="precursor_mass_tolerance" value="10.0"/>
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164 <param name="precursor_mass_units" value="ppm"/>
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165 <param name="fragment_bin_offset" value="0.0"/>
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166 <param name="fragment_bin_width" value="0.02"/>
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167 <param name="isotope_error" value=""/>
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168 <param name="run_percolator" value="false"/>
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169 <param name="enzyme" value="trypsin"/>
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170 <param name="digestion" value="full-digest"/>
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171 <param name="allowed_missed_cleavages" value="0"/>
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172 <param name="decoy_format" value="peptide-reverse"/>
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173 <param name="keep_terminal_aminos" value="NC"/>
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174 <param name="cterm_modifications" value=""/>
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175 <param name="nterm_modifications" value=""/>
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176 <param name="modifications" value=""/>
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177 <param name="test_fdr" value="0.01"/>
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178 <param name="train_fdr" value="0.01"/>
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179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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180 <output name="ctd_out" ftype="xml">
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181 <assert_contents>
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182 <is_valid_xml/>
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183 </assert_contents>
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184 </output>
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185 </test>
0
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186 </tests>
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187 <help><![CDATA[Identifies MS/MS spectra using Crux.
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188
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189
4
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190 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CruxAdapter.html]]></help>
0
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191 <expand macro="references"/>
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192 </tool>