Mercurial > repos > galaxyp > openms_triqlerconverter

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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 21:41:43 +0000
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fb0ebc6f97f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Converter to input for Triqler</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">TriqlerConverter</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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fb0ebc6f97f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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 &&
fb0ebc6f97f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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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f9675543622a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
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29 #end if
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30 #end if
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31
1
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32
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33 ## Main program call
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34
fb0ebc6f97f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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35 set -o pipefail &&
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36 @EXECUTABLE@ -write_ctd ./ &&
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37 python3 '$__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
0
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46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
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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($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
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52 #end if
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53 #end if
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54
1
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55
0
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56 ## Postprocessing
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57 && mv 'out/output.${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>
1
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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="-Triqler_condition" type="text" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
0
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69 <expand macro="list_string_san" name="Triqler_condition"/>
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70 </param>
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71 <expand macro="adv_opts_macro">
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72 <conditional name="reannotate_filenames_cond">
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73 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
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74 <option value="no">No: process all datasets jointly</option>
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75 <option value="yes">Yes: process each dataset in an independent job</option>
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76 </param>
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77 <when value="no">
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78 <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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79 </when>
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80 <when value="yes">
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81 <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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82 </when>
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83 </conditional>
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84 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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85 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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86 <expand macro="list_string_san" name="test"/>
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87 </param>
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88 </expand>
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89 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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91 </param>
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92 </inputs>
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93 <outputs>
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94 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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95 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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96 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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97 </data>
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98 </outputs>
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99 <tests/>
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100 <help><![CDATA[Converter to input for Triqler
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101
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102
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103 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TriqlerConverter.html]]></help>
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104 <expand macro="references"/>
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105 </tool>