Mercurial > repos > galaxyp > openms_idmerger

annotate IDMerger.xml @ 15:34e7afee141d 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 19:18:45 +0000
parents 978de6b97ca8
children
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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: [File Handling]-->
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4 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Merges several protein/peptide identification files into one file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMerger</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_cond.in &&
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18 #if $in_cond.in_select == "no"
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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20 ${' '.join(["ln -s '%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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21 #else
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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23 #end if
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24 mkdir out &&
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25 #if $add_to:
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26 mkdir add_to &&
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27 ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 -in
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37 #if $in_cond.in_select == "no"
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38 ${' '.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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39 #else
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40 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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41 #end if
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42 -out
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43 'out/output.${out_type}'
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44 #if $add_to:
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45 -add_to
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46 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)'
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47 #end if
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48
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49 ## Postprocessing
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50 && mv 'out/output.${out_type}' '$out'
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51 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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52 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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53 #end if]]></command>
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54 <configfiles>
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55 <inputs name="args_json" data_style="paths"/>
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56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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57 </configfiles>
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58 <inputs>
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59 <conditional name="in_cond">
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60 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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61 <option value="no">No: process all datasets jointly</option>
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62 <option value="yes">Yes: process each dataset in an independent job</option>
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63 </param>
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64 <when value="no">
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65 <param argument="-in" type="data" format="idxml,sqlite" multiple="true" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
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66 </when>
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67 <when value="yes">
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68 <param argument="-in" type="data" format="idxml,sqlite" multiple="false" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
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69 </when>
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70 </conditional>
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71 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
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72 <option value="idXML">idxml</option>
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73 <option value="oms">sqlite (oms)</option>
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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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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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><!-- TOPP_IDMerger_1 -->
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101 <test expect_num_outputs="2">
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102 <section name="adv_opts">
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103 <param name="force" value="false"/>
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104 <param name="test" value="true"/>
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105 </section>
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106 <conditional name="in_cond">
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107 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
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108 </conditional>
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109 <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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110 <param name="out_type" value="idXML"/>
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111 <param name="annotate_file_origin" value="true"/>
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112 <param name="pepxml_protxml" value="false"/>
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113 <param name="merge_proteins_add_PSMs" value="false"/>
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114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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115 <output name="ctd_out" ftype="xml">
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116 <assert_contents>
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117 <is_valid_xml/>
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118 </assert_contents>
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119 </output>
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120 </test>
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121 <!-- TOPP_IDMerger_2 -->
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122 <test expect_num_outputs="2">
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123 <section name="adv_opts">
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124 <param name="force" value="false"/>
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125 <param name="test" value="true"/>
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126 </section>
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127 <conditional name="in_cond">
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128 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
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129 </conditional>
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130 <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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131 <param name="out_type" value="idXML"/>
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132 <param name="annotate_file_origin" value="false"/>
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133 <param name="pepxml_protxml" value="true"/>
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134 <param name="merge_proteins_add_PSMs" value="false"/>
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135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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136 <output name="ctd_out" ftype="xml">
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137 <assert_contents>
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138 <is_valid_xml/>
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139 </assert_contents>
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140 </output>
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141 </test>
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142 <!-- TOPP_IDMerger_3 -->
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143 <test expect_num_outputs="2">
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144 <section name="adv_opts">
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145 <param name="force" value="false"/>
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146 <param name="test" value="true"/>
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147 </section>
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148 <conditional name="in_cond">
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149 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
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150 </conditional>
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151 <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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152 <param name="out_type" value="idXML"/>
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153 <param name="annotate_file_origin" value="false"/>
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154 <param name="pepxml_protxml" value="false"/>
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155 <param name="merge_proteins_add_PSMs" value="false"/>
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156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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157 <output name="ctd_out" ftype="xml">
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158 <assert_contents>
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159 <is_valid_xml/>
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160 </assert_contents>
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161 </output>
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162 </test>
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163 <!-- TOPP_IDMerger_4 -->
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164 <test expect_num_outputs="2">
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165 <section name="adv_opts">
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166 <param name="force" value="false"/>
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167 <param name="test" value="true"/>
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168 </section>
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169 <conditional name="in_cond">
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170 <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
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171 </conditional>
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172 <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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173 <param name="out_type" value="idXML"/>
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174 <param name="annotate_file_origin" value="false"/>
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175 <param name="pepxml_protxml" value="false"/>
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176 <param name="merge_proteins_add_PSMs" value="false"/>
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177 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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178 <output name="ctd_out" ftype="xml">
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179 <assert_contents>
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180 <is_valid_xml/>
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181 </assert_contents>
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182 </output>
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183 </test>
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184 <!-- TOPP_IDMerger_5 -->
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185 <test expect_num_outputs="2">
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186 <section name="adv_opts">
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187 <param name="force" value="false"/>
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188 <param name="test" value="true"/>
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189 </section>
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190 <conditional name="in_cond">
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191 <param name="in" value="IDMerger_2_input1.idXML"/>
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192 </conditional>
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193 <output name="out" file="IDMerger_5_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="add_to" value="IDMerger_5_input1.idXML"/>
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196 <param name="annotate_file_origin" value="false"/>
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197 <param name="pepxml_protxml" value="false"/>
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198 <param name="merge_proteins_add_PSMs" value="false"/>
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199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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200 <output name="ctd_out" ftype="xml">
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201 <assert_contents>
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202 <is_valid_xml/>
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203 </assert_contents>
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204 </output>
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205 </test>
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206 <!-- TOPP_IDMerger_6 -->
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207 <test expect_num_outputs="2">
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208 <section name="adv_opts">
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209 <param name="force" value="false"/>
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210 <param name="test" value="true"/>
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211 </section>
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212 <conditional name="in_cond">
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213 <param name="in" value="IDMerger_6_input1.oms,IDMerger_6_input2.oms"/>
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214 </conditional>
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215 <output name="out" file="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
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216 <param name="out_type" value="oms"/>
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217 <param name="annotate_file_origin" value="true"/>
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218 <param name="pepxml_protxml" value="false"/>
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219 <param name="merge_proteins_add_PSMs" value="false"/>
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220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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221 <output name="ctd_out" ftype="xml">
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222 <assert_contents>
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223 <is_valid_xml/>
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224 </assert_contents>
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225 </output>
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226 </test>
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227 <!-- TOPP_IDRipper_3_prep -->
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228 <test expect_num_outputs="2">
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229 <section name="adv_opts">
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230 <param name="force" value="false"/>
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231 <param name="test" value="true"/>
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232 </section>
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233 <conditional name="in_cond">
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234 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
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235 </conditional>
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236 <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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237 <param name="out_type" value="idXML"/>
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238 <param name="annotate_file_origin" value="true"/>
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239 <param name="pepxml_protxml" value="false"/>
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240 <param name="merge_proteins_add_PSMs" value="false"/>
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241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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242 <output name="ctd_out" ftype="xml">
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243 <assert_contents>
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244 <is_valid_xml/>
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245 </assert_contents>
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246 </output>
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247 </test>
11
64dbb1eb0048 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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248 </tests>
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249 <help><![CDATA[Merges several protein/peptide identification files into one file.
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250
75805008dd71 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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251
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252 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMerger.html]]></help>
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253 <expand macro="references"/>
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254 </tool>