Mercurial > repos > galaxyp > openms_msstatsconverter

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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 21:33:43 +0000
parents e3fb590554fd
children
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0dcd11bc33f8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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 Converter]-->
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3 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Converter to input for MSstats</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">MSstatsConverter</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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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir in_design &&
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19 cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
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20 mkdir out &&
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21 ## advanced options
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22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
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23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
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24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
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25 mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} &&
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26 ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
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27 #else
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28 cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
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29 #end if
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30 #end if
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33 ## Main program call
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34
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35 set -o pipefail &&
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36 @EXECUTABLE@ -write_ctd ./ &&
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37 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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38 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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39 -in
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40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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41 -in_design
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42 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
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43 -out
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44 'out/output.${gxy2omsext("csv")}'
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45 ## advanced options
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46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
0
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47 -reannotate_filenames
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48 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
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49 ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
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50 #else
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51 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
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52 #end if
0
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53 #end if
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54
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55
0
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56 ## Postprocessing
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57 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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58 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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59 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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60 #end if]]></command>
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61 <configfiles>
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62 <inputs name="args_json" data_style="paths"/>
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63 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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64 </configfiles>
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65 <inputs>
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66 <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
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67 <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
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68 <param argument="-method" type="select" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
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69 <option value="LFQ" selected="true">LFQ</option>
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70 <option value="ISO">ISO</option>
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71 <expand macro="list_string_san" name="method"/>
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72 </param>
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73 <param argument="-msstats_bioreplicate" type="text" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
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74 <expand macro="list_string_san" name="msstats_bioreplicate"/>
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75 </param>
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76 <param argument="-msstats_condition" type="text" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
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77 <expand macro="list_string_san" name="msstats_condition"/>
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78 </param>
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79 <param argument="-msstats_mixture" type="text" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
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80 <expand macro="list_string_san" name="msstats_mixture"/>
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81 </param>
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82 <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
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83 <expand macro="adv_opts_macro">
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84 <conditional name="reannotate_filenames_cond">
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85 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
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86 <option value="no">No: process all datasets jointly</option>
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87 <option value="yes">Yes: process each dataset in an independent job</option>
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88 </param>
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89 <when value="no">
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90 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
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91 </when>
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92 <when value="yes">
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93 <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
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94 </when>
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95 </conditional>
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96 <param argument="-retention_time_summarization_method" type="select" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
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97 <option value="manual">manual</option>
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98 <option value="max" selected="true">max</option>
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99 <option value="min">min</option>
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100 <option value="mean">mean</option>
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101 <option value="sum">sum</option>
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102 <expand macro="list_string_san" name="retention_time_summarization_method"/>
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103 </param>
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104 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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105 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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106 <expand macro="list_string_san" name="test"/>
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107 </param>
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108 </expand>
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109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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110 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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111 </param>
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112 </inputs>
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113 <outputs>
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114 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <!-- TOPP_MSstatsConverter_1 -->
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121 <test expect_num_outputs="2">
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122 <section name="adv_opts">
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123 <param name="retention_time_summarization_method" value="max"/>
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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 <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
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128 <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
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129 <param name="method" value="LFQ"/>
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130 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
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131 <param name="msstats_condition" value="MSstats_Condition"/>
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132 <param name="msstats_mixture" value="MSstats_Mixture"/>
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133 <param name="labeled_reference_peptides" value="false"/>
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134 <output name="out" value="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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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 <assert_stdout>
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142 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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143 </assert_stdout>
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144 </test>
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145 <!-- TOPP_MSstatsConverter_2 -->
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146 <test expect_num_outputs="2">
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147 <section name="adv_opts">
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148 <param name="retention_time_summarization_method" value="manual"/>
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149 <param name="force" value="false"/>
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150 <param name="test" value="true"/>
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151 </section>
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152 <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
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153 <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
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154 <param name="method" value="ISO"/>
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155 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
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156 <param name="msstats_condition" value="MSstats_Condition"/>
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157 <param name="msstats_mixture" value="MSstats_Mixture"/>
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158 <param name="labeled_reference_peptides" value="false"/>
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159 <output name="out" value="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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161 <output name="ctd_out" ftype="xml">
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162 <assert_contents>
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163 <is_valid_xml/>
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164 </assert_contents>
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165 </output>
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166 <assert_stdout>
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167 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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168 </assert_stdout>
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169 </test>
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170 <!-- TOPP_MSstatsConverter_3 -->
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171 <test expect_num_outputs="2">
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172 <section name="adv_opts">
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173 <param name="retention_time_summarization_method" value="manual"/>
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174 <param name="force" value="false"/>
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175 <param name="test" value="true"/>
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176 </section>
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177 <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
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178 <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
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179 <param name="method" value="ISO"/>
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180 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
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181 <param name="msstats_condition" value="MSstats_Condition"/>
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182 <param name="msstats_mixture" value="MSstats_Mixture"/>
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183 <param name="labeled_reference_peptides" value="false"/>
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184 <output name="out" value="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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186 <output name="ctd_out" ftype="xml">
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187 <assert_contents>
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188 <is_valid_xml/>
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189 </assert_contents>
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190 </output>
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191 <assert_stdout>
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192 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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193 </assert_stdout>
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194 </test>
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195 </tests>
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196 <help><![CDATA[Converter to input for MSstats
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197
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198
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199 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSstatsConverter.html]]></help>
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200 <expand macro="references"/>
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201 </tool>