Mercurial > repos > galaxyp > openms_idmerger

annotate IDMerger.xml @ 16:bdcdd2a5ea43 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:40:49 +0000
parents 34e7afee141d
children
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1 <!--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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2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
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3 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Merges several protein/peptide identification files into one file</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">IDMerger</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir out &&
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24 #if $add_to:
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25 mkdir add_to &&
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26 cp '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
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27 #end if
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 #if $in_cond.in_select == "no"
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37 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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38 #else
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39 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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40 #end if
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41 -out
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42 'out/output.${out_type}'
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43 #if $add_to:
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44 -add_to
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45 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)'
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46 #end if
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47
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48 ## Postprocessing
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49 && mv 'out/output.${out_type}' '$out'
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50 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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51 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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52 #end if]]></command>
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53 <configfiles>
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54 <inputs name="args_json" data_style="paths"/>
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55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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56 </configfiles>
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57 <inputs>
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58 <conditional name="in_cond">
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59 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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60 <option value="no">No: process all datasets jointly</option>
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61 <option value="yes">Yes: process each dataset in an independent job</option>
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62 </param>
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63 <when value="no">
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64 <param argument="-in" type="data" format="idxml,sqlite" multiple="true" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
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65 </when>
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66 <when value="yes">
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67 <param argument="-in" type="data" format="idxml,sqlite" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
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68 </when>
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69 </conditional>
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70 <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
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71 <option value="idXML">idxml</option>
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72 <option value="oms">sqlite (oms)</option>
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73 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
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74 <expand macro="list_string_san" name="out_type"/>
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75 </param>
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76 <param argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/>
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77 <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output only" help=""/>
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78 <param argument="-pepxml_protxml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
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79 <param argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
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80 <expand macro="adv_opts_macro">
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81 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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82 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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83 <expand macro="list_string_san" name="test"/>
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84 </param>
0
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85 </expand>
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86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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87 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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88 </param>
0
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89 </inputs>
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90 <outputs>
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91 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
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92 <change_format>
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93 <when input="out_type" value="oms" format="sqlite"/>
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94 </change_format>
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95 </data>
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96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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98 </data>
0
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99 </outputs>
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100 <tests>
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101 <!-- TOPP_IDMerger_1 -->
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102 <test expect_num_outputs="2">
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103 <section name="adv_opts">
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104 <param name="force" value="false"/>
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105 <param name="test" value="true"/>
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106 </section>
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107 <conditional name="in_cond">
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108 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
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109 </conditional>
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110 <output name="out" value="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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111 <param name="out_type" value="idXML"/>
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112 <param name="annotate_file_origin" value="true"/>
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113 <param name="pepxml_protxml" value="false"/>
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114 <param name="merge_proteins_add_PSMs" value="false"/>
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115 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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116 <output name="ctd_out" ftype="xml">
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117 <assert_contents>
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118 <is_valid_xml/>
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119 </assert_contents>
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120 </output>
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121 <assert_stdout>
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122 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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123 </assert_stdout>
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124 </test>
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125 <!-- TOPP_IDMerger_2 -->
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126 <test expect_num_outputs="2">
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127 <section name="adv_opts">
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128 <param name="force" value="false"/>
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129 <param name="test" value="true"/>
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130 </section>
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131 <conditional name="in_cond">
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132 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
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133 </conditional>
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134 <output name="out" value="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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135 <param name="out_type" value="idXML"/>
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136 <param name="annotate_file_origin" value="false"/>
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137 <param name="pepxml_protxml" value="true"/>
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138 <param name="merge_proteins_add_PSMs" value="false"/>
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139 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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140 <output name="ctd_out" ftype="xml">
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141 <assert_contents>
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142 <is_valid_xml/>
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143 </assert_contents>
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144 </output>
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145 <assert_stdout>
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146 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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147 </assert_stdout>
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148 </test>
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149 <!-- TOPP_IDMerger_3 -->
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150 <test expect_num_outputs="2">
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151 <section name="adv_opts">
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152 <param name="force" value="false"/>
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153 <param name="test" value="true"/>
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154 </section>
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155 <conditional name="in_cond">
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156 <param name="in" value="IDMerger_1_input1_0.idXML,IDMerger_1_input1_1.idXML"/>
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157 </conditional>
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158 <output name="out" value="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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159 <param name="out_type" value="idXML"/>
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160 <param name="annotate_file_origin" value="false"/>
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161 <param name="pepxml_protxml" value="false"/>
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162 <param name="merge_proteins_add_PSMs" value="false"/>
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163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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164 <output name="ctd_out" ftype="xml">
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165 <assert_contents>
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166 <is_valid_xml/>
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167 </assert_contents>
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168 </output>
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169 <assert_stdout>
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170 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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171 </assert_stdout>
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172 </test>
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173 <!-- TOPP_IDMerger_4 -->
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174 <test expect_num_outputs="2">
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175 <section name="adv_opts">
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176 <param name="force" value="false"/>
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177 <param name="test" value="true"/>
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178 </section>
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179 <conditional name="in_cond">
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180 <param name="in" value="degenerated_empty_0.idXML,degenerated_empty_1.idXML"/>
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181 </conditional>
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182 <output name="out" value="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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183 <param name="out_type" value="idXML"/>
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184 <param name="annotate_file_origin" value="false"/>
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185 <param name="pepxml_protxml" value="false"/>
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186 <param name="merge_proteins_add_PSMs" value="false"/>
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187 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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188 <output name="ctd_out" ftype="xml">
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189 <assert_contents>
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190 <is_valid_xml/>
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191 </assert_contents>
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192 </output>
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193 <assert_stdout>
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194 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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195 </assert_stdout>
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196 </test>
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197 <!-- TOPP_IDMerger_5 -->
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198 <test expect_num_outputs="2">
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199 <section name="adv_opts">
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200 <param name="force" value="false"/>
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201 <param name="test" value="true"/>
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202 </section>
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203 <conditional name="in_cond">
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204 <param name="in" value="IDMerger_2_input1.idXML"/>
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205 </conditional>
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206 <output name="out" value="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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207 <param name="out_type" value="idXML"/>
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208 <param name="add_to" value="IDMerger_5_input1.idXML"/>
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209 <param name="annotate_file_origin" value="false"/>
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210 <param name="pepxml_protxml" value="false"/>
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211 <param name="merge_proteins_add_PSMs" value="false"/>
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212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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213 <output name="ctd_out" ftype="xml">
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214 <assert_contents>
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215 <is_valid_xml/>
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216 </assert_contents>
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217 </output>
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218 <assert_stdout>
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219 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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220 </assert_stdout>
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221 </test>
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222 <!-- TOPP_IDMerger_6 -->
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223 <test expect_num_outputs="2">
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224 <section name="adv_opts">
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225 <param name="force" value="false"/>
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226 <param name="test" value="true"/>
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227 </section>
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228 <conditional name="in_cond">
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229 <param name="in" value="IDMerger_6_input1.oms,IDMerger_6_input2.oms"/>
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230 </conditional>
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231 <output name="out" value="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
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232 <param name="out_type" value="oms"/>
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233 <param name="annotate_file_origin" value="true"/>
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234 <param name="pepxml_protxml" value="false"/>
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235 <param name="merge_proteins_add_PSMs" value="false"/>
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236 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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237 <output name="ctd_out" ftype="xml">
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238 <assert_contents>
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239 <is_valid_xml/>
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240 </assert_contents>
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241 </output>
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242 <assert_stdout>
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243 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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244 </assert_stdout>
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245 </test>
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246 <!-- TOPP_IDRipper_3_prep -->
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247 <test expect_num_outputs="2">
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248 <section name="adv_opts">
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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 <conditional name="in_cond">
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253 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
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254 </conditional>
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255 <output name="out" value="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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256 <param name="out_type" value="idXML"/>
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257 <param name="annotate_file_origin" value="true"/>
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258 <param name="pepxml_protxml" value="false"/>
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259 <param name="merge_proteins_add_PSMs" value="false"/>
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260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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261 <output name="ctd_out" ftype="xml">
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262 <assert_contents>
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263 <is_valid_xml/>
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264 </assert_contents>
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265 </output>
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266 <assert_stdout>
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267 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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268 </assert_stdout>
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269 </test>
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270 </tests>
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271 <help><![CDATA[Merges several protein/peptide identification files into one file.
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272
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273
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274 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMerger.html]]></help>
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275 <expand macro="references"/>
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276 </tool>