Mercurial > repos > galaxyp > openms_qcembedder

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 19:02:06 +0000
parents b08552872ca6
children
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3aa8f9243d8b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [Utilities]-->
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4 <tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Attaches a table or an image to a given qc parameter.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">QCEmbedder</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 #if $in:
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20 mkdir in &&
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21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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22 #end if
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23 #if $run:
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24 mkdir run &&
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25 ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
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26 #end if
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27 #if $plot:
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28 mkdir plot &&
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29 ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
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30 #end if
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31 #if $table:
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32 mkdir table &&
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33 ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
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34 #end if
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35 mkdir out &&
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7f5b37bcb7bb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 ## Main program call
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38
7f5b37bcb7bb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 #if $in:
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44 -in
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45 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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46 #end if
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47 #if $run:
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48 -run
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49 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)'
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50 #end if
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51 #if $plot:
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52 -plot
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53 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)'
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54 #end if
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55 #if $table:
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56 -table
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57 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)'
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58 #end if
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59 -out
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60 'out/output.${gxy2omsext("qcml")}'
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61
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62 ## Postprocessing
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63 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
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64 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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65 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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66 #end if]]></command>
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67 <configfiles>
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68 <inputs name="args_json" data_style="paths"/>
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69 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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70 </configfiles>
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71 <inputs>
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72 <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
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73 <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
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74 <expand macro="list_string_san"/>
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75 </param>
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76 <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
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77 <expand macro="list_string_san"/>
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78 </param>
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79 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
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80 <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="">
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81 <expand macro="list_string_san"/>
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82 </param>
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83 <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/>
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84 <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
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85 <expand macro="adv_opts_macro">
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86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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88 <expand macro="list_string_san"/>
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89 </param>
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90 </expand>
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91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
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97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <expand macro="autotest_QCEmbedder"/>
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103 <expand macro="manutest_QCEmbedder"/>
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104 </tests>
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105 <help><![CDATA[Attaches a table or an image to a given qc parameter.
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106
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107
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108 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCEmbedder.html]]></help>
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109 <expand macro="references"/>
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110 </tool>