Mercurial > repos > galaxyp > openms_qccalculator

annotate QCCalculator.xml @ 11:044adca691a7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:02:07 +0000
parents 8bcc0d2ad96e
children d0607dfea8fa
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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="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">QCCalculator</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 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if $id:
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23 mkdir id &&
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24 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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25 #end if
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26 #if $feature:
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27 mkdir feature &&
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28 ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
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29 #end if
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30 #if $consensus:
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31 mkdir consensus &&
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32 ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
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33 #end if
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35 ## Main program call
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37 set -o pipefail &&
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38 @EXECUTABLE@ -write_ctd ./ &&
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39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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41 -in
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42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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43 -out
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44 'out/output.${gxy2omsext("qcml")}'
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45 #if $id:
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46 -id
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47 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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48 #end if
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49 #if $feature:
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50 -feature
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51 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)'
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52 #end if
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53 #if $consensus:
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54 -consensus
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55 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)'
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56 #end if
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57
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58 ## Postprocessing
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59 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
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60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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61 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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62 #end if]]></command>
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63 <configfiles>
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64 <inputs name="args_json" data_style="paths"/>
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65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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66 </configfiles>
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67 <inputs>
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68 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
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69 <param name="id" argument="-id" type="data" format="idxml" optional="true" label="Input idXML file containing the identifications" help="Your identifications will be exported in an easy-to-read format select idxml data sets(s)"/>
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70 <param name="feature" argument="-feature" type="data" format="featurexml" optional="true" label="feature input file (this is relevant for most QC issues)" help=" select featurexml data sets(s)"/>
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71 <param name="consensus" argument="-consensus" type="data" format="consensusxml" optional="true" label="consensus input file (this is only used for charge state deconvoluted output" help="Use the consensusXML output form the DeCharger) select consensusxml data sets(s)"/>
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72 <param name="remove_duplicate_features" argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/>
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73 <expand macro="adv_opts_macro">
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74 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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75 <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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76 <expand macro="list_string_san"/>
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77 </param>
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78 </expand>
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79 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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81 </param>
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82 </inputs>
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83 <outputs>
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84 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
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85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <expand macro="autotest_QCCalculator"/>
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91 <expand macro="manutest_QCCalculator"/>
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92 </tests>
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93 <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
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94
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95
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96 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCCalculator.html]]></help>
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97 <expand macro="references"/>
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98 </tool>