Mercurial > repos > galaxyp > openms_qualitycontrol

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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 21:46:38 +0000
parents bd210b86fb5d
children
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e2f683fcd6bd "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.-->
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2 <!--Proposed Tool Section: [Quality Control]-->
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bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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3 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get</description>
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5 <macros>
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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6 <token name="@EXECUTABLE@">QualityControl</token>
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7 <import>macros.xml</import>
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8 </macros>
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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9 <expand macro="requirements"/>
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="stdio"/>
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 #import re
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 ## Preprocessing
e2f683fcd6bd "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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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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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 #if $in_raw_cond.in_raw:
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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19 mkdir in_raw_cond.in_raw &&
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20 #if $in_raw_cond.in_raw_select == "no"
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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21 mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} &&
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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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22 ${' '.join(["cp '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
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bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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23 #else
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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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24 cp '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
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bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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25 #end if
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26 #end if
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27 #if $in_postFDR_cond.in_postFDR:
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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28 mkdir in_postFDR_cond.in_postFDR &&
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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29 #if $in_postFDR_cond.in_postFDR_select == "no"
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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30 mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} &&
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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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31 ${' '.join(["cp '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
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32 #else
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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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33 cp '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
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bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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34 #end if
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35 #end if
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36 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 mkdir out &&
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38 #end if
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39 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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40 mkdir out_cm &&
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41 #end if
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42 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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43 mkdir out_feat &&
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44 mkdir ${' '.join(["'out_feat/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} &&
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45 #end if
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46 #if $in_contaminants:
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47 mkdir in_contaminants &&
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48 cp '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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49 #end if
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50 #if $in_fasta:
ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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51 mkdir in_fasta &&
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52 cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
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53 #end if
4
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54 #if $in_trafo_cond.in_trafo:
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55 mkdir in_trafo_cond.in_trafo &&
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56 #if $in_trafo_cond.in_trafo_select == "no"
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57 mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} &&
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ea02cc72f0b9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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58 ${' '.join(["cp '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
4
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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59 #else
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60 cp '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
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bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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61 #end if
0
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62 #end if
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63
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 ## Main program call
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65
e2f683fcd6bd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 set -o pipefail &&
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67 @EXECUTABLE@ -write_ctd ./ &&
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68 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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69 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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70 -in_cm
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71 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
4
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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72 #if $in_raw_cond.in_raw:
0
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73 -in_raw
4
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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74 #if $in_raw_cond.in_raw_select == "no"
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75 ${' '.join(["'in_raw_cond.in_raw/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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76 #else
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77 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)'
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78 #end if
0
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79 #end if
4
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80 #if $in_postFDR_cond.in_postFDR:
0
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81 -in_postFDR
4
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82 #if $in_postFDR_cond.in_postFDR_select == "no"
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83 ${' '.join(["'in_postFDR_cond.in_postFDR/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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84 #else
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85 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)'
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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86 #end if
0
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87 #end if
2
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88 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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89 -out
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90 'out/output.${gxy2omsext("mztab")}'
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91 #end if
0
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92 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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93 -out_cm
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94 'out_cm/output.${gxy2omsext("consensusxml")}'
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95 #end if
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96 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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97 -out_feat
4
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98 ${' '.join(["'out_feat/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("featurexml")) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
0
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99 #end if
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100 #if $in_contaminants:
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101 -in_contaminants
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102 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
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103 #end if
5
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104 #if $in_fasta:
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105 -in_fasta
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106 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)'
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107 #end if
4
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108 #if $in_trafo_cond.in_trafo:
0
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109 -in_trafo
4
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110 #if $in_trafo_cond.in_trafo_select == "no"
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111 ${' '.join(["'in_trafo_cond.in_trafo/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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112 #else
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113 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)'
bd210b86fb5d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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114 #end if
0
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115 #end if
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116 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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117 | tee '$stdout'
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118 #end if
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119
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120 ## Postprocessing
2
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121 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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122 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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123 #end if
0
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124 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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125 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
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126 #end if
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127 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4
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128 ${' '.join(["&& mv -n 'out_feat/%(bn)s/%(id)s.%(gext)s' 'out_feat/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("featurexml")} for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
0
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129 #end if
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130 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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131 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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132 #end if]]></command>
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133 <configfiles>
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134 <inputs name="args_json" data_style="paths"/>
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135 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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136 </configfiles>
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137 <inputs>
5
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138 <param argument="-in_cm" type="data" format="consensusxml" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
4
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139 <conditional name="in_raw_cond">
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140 <param name="in_raw_select" type="select" label="Run tool in batch mode for -in_raw">
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141 <option value="no">No: process all datasets jointly</option>
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142 <option value="yes">Yes: process each dataset in an independent job</option>
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143 </param>
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144 <when value="no">
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145 <param argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
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146 </when>
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147 <when value="yes">
5
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148 <param argument="-in_raw" type="data" format="mzml" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
4
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149 </when>
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150 </conditional>
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151 <conditional name="in_postFDR_cond">
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152 <param name="in_postFDR_select" type="select" label="Run tool in batch mode for -in_postFDR">
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153 <option value="no">No: process all datasets jointly</option>
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154 <option value="yes">Yes: process each dataset in an independent job</option>
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155 </param>
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156 <when value="no">
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157 <param argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
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158 </when>
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159 <when value="yes">
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160 <param argument="-in_postFDR" type="data" format="featurexml" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
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161 </when>
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162 </conditional>
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163 <param argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
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164 <param argument="-in_fasta" type="data" format="fasta" optional="true" label="FASTA file used during MS/MS identification (including decoys)" help="If the protein description contains 'GN=...' then gene names will be extracted select fasta data sets(s)"/>
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165 <conditional name="in_trafo_cond">
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166 <param name="in_trafo_select" type="select" label="Run tool in batch mode for -in_trafo">
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167 <option value="no">No: process all datasets jointly</option>
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168 <option value="yes">Yes: process each dataset in an independent job</option>
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169 </param>
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170 <when value="no">
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171 <param argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
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172 </when>
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173 <when value="yes">
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174 <param argument="-in_trafo" type="data" format="trafoxml" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
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175 </when>
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176 </conditional>
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177 <param argument="-out_evd" type="text" optional="true" value="" label="If a Path is given, a MQEvidence txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
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178 <expand macro="list_string_san" name="out_evd"/>
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179 </param>
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180 <param argument="-out_msms" type="text" optional="true" value="" label="If a Path is given, a MQMsms txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
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181 <expand macro="list_string_san" name="out_msms"/>
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182 </param>
0
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183 <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
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184 <param name="unit" argument="-FragmentMassError:unit" type="select" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
0
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185 <option value="auto" selected="true">auto</option>
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186 <option value="ppm">ppm</option>
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187 <option value="da">da</option>
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188 <expand macro="list_string_san" name="unit"/>
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189 </param>
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190 <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
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191 </section>
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192 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
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193 <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
0
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194 </section>
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195 <expand macro="adv_opts_macro">
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196 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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197 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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198 <expand macro="list_string_san" name="test"/>
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199 </param>
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200 </expand>
2
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201 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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202 <option value="out_FLAG">out (Output mzTab with QC information)</option>
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203 <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option>
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204 <option value="out_feat_FLAG">out_feat (FeatureXMLs with QC information (as metavalues))</option>
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205 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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206 </param>
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207 </inputs>
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208 <outputs>
2
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209 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab">
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210 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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211 </data>
0
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212 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
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213 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
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214 </data>
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215 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
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216 <discover_datasets directory="out_feat" recurse="true" format="featurexml" pattern="__name__"/>
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217 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
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218 </collection>
2
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219 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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220 <filter>OPTIONAL_OUTPUTS is None</filter>
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221 </data>
0
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222 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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223 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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224 </data>
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225 </outputs>
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226 <tests>
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227 <!-- TOPP_QualityControl_1 -->
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228 <test expect_num_outputs="3">
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229 <section name="adv_opts">
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230 <param name="force" value="false"/>
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231 <param name="test" value="true"/>
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232 </section>
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233 <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
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234 <conditional name="in_raw_cond">
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235 <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
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236 </conditional>
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237 <conditional name="in_postFDR_cond">
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238 <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
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239 </conditional>
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240 <output name="out" value="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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241 <output name="out_cm" value="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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242 <param name="in_contaminants" value="QualityControl_1.fasta"/>
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243 <param name="in_fasta" value="PeptideIndexer_1.fasta"/>
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244 <conditional name="in_trafo_cond">
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245 <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
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246 </conditional>
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247 <param name="out_evd" value=""/>
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248 <param name="out_msms" value=""/>
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249 <section name="FragmentMassError">
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250 <param name="unit" value="auto"/>
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251 <param name="tolerance" value="20.0"/>
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252 </section>
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253 <section name="MS2_id_rate">
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254 <param name="assume_all_target" value="false"/>
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255 </section>
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256 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
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257 <output name="ctd_out" ftype="xml">
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258 <assert_contents>
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259 <is_valid_xml/>
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260 </assert_contents>
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261 </output>
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262 <assert_stdout>
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263 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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264 </assert_stdout>
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265 </test>
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266 </tests>
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267 <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
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268
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269
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270 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QualityControl.html]]></help>
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271 <expand macro="references"/>
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272 </tool>