Mercurial > repos > galaxyp > openms_gnpsexport

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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 21:33:13 +0000
parents 2da14ae3844a
children
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22885d201eb8 "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="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">GNPSExport</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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22885d201eb8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 ## Preprocessing
22885d201eb8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 mkdir in_cm &&
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17 cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
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18 mkdir in_mzml_cond.in_mzml &&
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19 #if $in_mzml_cond.in_mzml_select == "no"
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20 mkdir ${' '.join(["'in_mzml_cond.in_mzml/%s'" % (i) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} &&
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21 ${' '.join(["cp '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
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22 #else
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23 cp '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' &&
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24 #end if
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25 mkdir out &&
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26 mkdir out_quantification &&
87a970d1514b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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27 #if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
87a970d1514b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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28 mkdir out_pairs &&
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29 #end if
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30 #if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir out_meta_values &&
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32 #end if
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34 ## Main program call
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36 set -o pipefail &&
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37 @EXECUTABLE@ -write_ctd ./ &&
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38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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40 -in_cm
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41 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
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42 -in_mzml
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43 #if $in_mzml_cond.in_mzml_select == "no"
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44 ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
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45 #else
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46 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)'
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47 #end if
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48 -out
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49 'out/output.${gxy2omsext("mgf")}'
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50 -out_quantification
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51 'out_quantification/output.${gxy2omsext("txt")}'
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52 #if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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53 -out_pairs
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54 'out_pairs/output.${gxy2omsext("csv")}'
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55 #end if
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56 #if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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57 -out_meta_values
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58 'out_meta_values/output.${gxy2omsext("tabular")}'
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59 #end if
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60 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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61 | tee '$stdout'
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62 #end if
0
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63
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64 ## Postprocessing
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65 && mv 'out/output.${gxy2omsext("mgf")}' '$out'
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66 && mv 'out_quantification/output.${gxy2omsext("txt")}' '$out_quantification'
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67 #if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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68 && mv 'out_pairs/output.${gxy2omsext("csv")}' '$out_pairs'
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69 #end if
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70 #if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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71 && mv 'out_meta_values/output.${gxy2omsext("tabular")}' '$out_meta_values'
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72 #end if
0
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73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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74 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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75 #end if]]></command>
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76 <configfiles>
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77 <inputs name="args_json" data_style="paths"/>
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78 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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79 </configfiles>
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80 <inputs>
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81 <param argument="-in_cm" type="data" format="consensusxml" label="Input consensusXML file containing only consensusElements with &quot;peptide&quot; annotations" help=" select consensusxml data sets(s)"/>
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82 <conditional name="in_mzml_cond">
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83 <param name="in_mzml_select" type="select" label="Run tool in batch mode for -in_mzml">
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84 <option value="no">No: process all datasets jointly</option>
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85 <option value="yes">Yes: process each dataset in an independent job</option>
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86 </param>
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87 <when value="no">
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88 <param argument="-in_mzml" type="data" format="mzml" multiple="true" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
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89 </when>
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90 <when value="yes">
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91 <param argument="-in_mzml" type="data" format="mzml" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
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92 </when>
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93 </conditional>
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94 <param argument="-output_type" type="select" label="specificity of mgf output information" help="">
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95 <option value="merged_spectra">merged_spectra</option>
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96 <option value="most_intense" selected="true">most_intense</option>
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97 <expand macro="list_string_san" name="output_type"/>
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98 </param>
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99 <param argument="-peptide_cutoff" type="integer" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/>
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100 <param argument="-ms2_bin_size" type="float" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/>
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101 <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per consensusElement" help="" expanded="false">
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102 <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/>
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103 </section>
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104 <expand macro="adv_opts_macro">
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105 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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106 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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107 <expand macro="list_string_san" name="test"/>
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108 </param>
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109 </expand>
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110 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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111 <option value="out_pairs_FLAG">out_pairs (Output supplementary pairs table for IIMN)</option>
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112 <option value="out_meta_values_FLAG">out_meta_values (Output meta value file)</option>
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113 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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114 </param>
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115 </inputs>
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116 <outputs>
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117 <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/>
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118 <data name="out_quantification" label="${tool.name} on ${on_string}: out_quantification" format="txt"/>
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119 <data name="out_pairs" label="${tool.name} on ${on_string}: out_pairs" format="csv">
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120 <filter>OPTIONAL_OUTPUTS is not None and "out_pairs_FLAG" in OPTIONAL_OUTPUTS</filter>
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121 </data>
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122 <data name="out_meta_values" label="${tool.name} on ${on_string}: out_meta_values" format="tabular">
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123 <filter>OPTIONAL_OUTPUTS is not None and "out_meta_values_FLAG" in OPTIONAL_OUTPUTS</filter>
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124 </data>
0
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125 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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126 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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127 </data>
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128 </outputs>
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129 <tests>
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130 <!-- TOPP_GNPSExport_1 -->
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131 <test expect_num_outputs="3">
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132 <section name="adv_opts">
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133 <param name="force" value="false"/>
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134 <param name="test" value="true"/>
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135 </section>
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136 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/>
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137 <conditional name="in_mzml_cond">
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138 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
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139 </conditional>
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140 <output name="out" value="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
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141 <output name="out_quantification" value="GNPSExport_1_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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142 <param name="output_type" value="most_intense"/>
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143 <param name="peptide_cutoff" value="10"/>
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144 <param name="ms2_bin_size" value="2.0"/>
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145 <section name="merged_spectra">
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146 <param name="cos_similarity" value="0.85"/>
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147 </section>
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148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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149 <output name="ctd_out" ftype="xml">
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150 <assert_contents>
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151 <is_valid_xml/>
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152 </assert_contents>
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153 </output>
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154 <assert_stdout>
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155 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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156 </assert_stdout>
4
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157 </test>
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158 <!-- TOPP_GNPSExport_2 -->
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159 <test expect_num_outputs="3">
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160 <section name="adv_opts">
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161 <param name="force" value="false"/>
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162 <param name="test" value="true"/>
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163 </section>
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164 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/>
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165 <conditional name="in_mzml_cond">
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166 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
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167 </conditional>
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168 <output name="out" value="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
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169 <output name="out_quantification" value="GNPSExport_2_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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170 <param name="output_type" value="merged_spectra"/>
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171 <param name="peptide_cutoff" value="10"/>
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172 <param name="ms2_bin_size" value="2.0"/>
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173 <section name="merged_spectra">
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174 <param name="cos_similarity" value="0.85"/>
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175 </section>
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176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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177 <output name="ctd_out" ftype="xml">
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178 <assert_contents>
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179 <is_valid_xml/>
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180 </assert_contents>
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181 </output>
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182 <assert_stdout>
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183 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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184 </assert_stdout>
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185 </test>
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186 <!-- TOPP_GNPSExport_3 -->
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187 <test expect_num_outputs="3">
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188 <section name="adv_opts">
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189 <param name="force" value="false"/>
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190 <param name="test" value="true"/>
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191 </section>
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192 <param name="in_cm" value="GNPSExport_cons1.consensusXML"/>
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193 <conditional name="in_mzml_cond">
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194 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
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195 </conditional>
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196 <output name="out" value="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
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197 <output name="out_quantification" value="GNPSExport_3_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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198 <param name="output_type" value="most_intense"/>
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199 <param name="peptide_cutoff" value="10"/>
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200 <param name="ms2_bin_size" value="0.02"/>
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201 <section name="merged_spectra">
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202 <param name="cos_similarity" value="0.85"/>
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203 </section>
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204 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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205 <output name="ctd_out" ftype="xml">
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206 <assert_contents>
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207 <is_valid_xml/>
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208 </assert_contents>
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209 </output>
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210 <assert_stdout>
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211 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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212 </assert_stdout>
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213 </test>
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214 <!-- TOPP_GNPSExport_4 -->
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215 <test expect_num_outputs="5">
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216 <section name="adv_opts">
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217 <param name="force" value="false"/>
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218 <param name="test" value="true"/>
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219 </section>
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220 <param name="in_cm" value="GNPSExport_cons2.consensusXML"/>
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221 <conditional name="in_mzml_cond">
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222 <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
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223 </conditional>
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224 <output name="out" value="GNPSExport_4_out.tmp" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
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225 <output name="out_quantification" value="GNPSExport_4_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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226 <output name="out_pairs" value="GNPSExport_4_out_pairs.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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227 <output name="out_meta_values" value="GNPSExport_4_out_meta_values.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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228 <param name="output_type" value="most_intense"/>
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229 <param name="peptide_cutoff" value="5"/>
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230 <param name="ms2_bin_size" value="0.019999999552965"/>
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231 <section name="merged_spectra">
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232 <param name="cos_similarity" value="0.9"/>
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233 </section>
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234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pairs_FLAG,out_meta_values_FLAG"/>
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235 <output name="ctd_out" ftype="xml">
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236 <assert_contents>
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237 <is_valid_xml/>
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238 </assert_contents>
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239 </output>
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240 <assert_stdout>
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241 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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242 </assert_stdout>
4
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243 </test>
0
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244 </tests>
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245 <help><![CDATA[Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.
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246 See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms
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247
4
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248
5
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249 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_GNPSExport.html]]></help>
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250 <expand macro="references"/>
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251 </tool>