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annotate QualityControl.xml @ 0:be0252d4f146 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:50:42 +0000
parents
children 1ad274072c05
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0
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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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.-->
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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3 <!--Proposed Tool Section: [Quality Control]-->
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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4 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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5 <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>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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6 <macros>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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7 <token name="@EXECUTABLE@">QualityControl</token>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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8 <import>macros.xml</import>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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9 <import>macros_autotest.xml</import>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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10 <import>macros_test.xml</import>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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11 </macros>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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12 <expand macro="requirements"/>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 <expand macro="stdio"/>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 @EXT_FOO@
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 #import re
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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17
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ## Preprocessing
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 mkdir in_cm &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 #if $in_raw:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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22 mkdir in_raw &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 ${ ' '.join(["ln -s '%s' 'in_raw/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _]) }
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 #if $in_postFDR:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 mkdir in_postFDR &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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27 ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 mkdir out &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 mkdir out_cm &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 mkdir out_feat &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 #if $in_contaminants:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 mkdir in_contaminants &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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38 ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 #if $in_trafo:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 mkdir in_trafo &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 ${ ' '.join(["ln -s '%s' 'in_trafo/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _]) }
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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45 ## Main program call
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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46
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 set -o pipefail &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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48 @EXECUTABLE@ -write_ctd ./ &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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50 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 -in_cm
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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52 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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53 #if $in_raw:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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54 -in_raw
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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55 ${' '.join(["'in_raw/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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56 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 #if $in_postFDR:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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58 -in_postFDR
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 -out
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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62 'out/output.${gxy2omsext("mztab")}'
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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64 -out_cm
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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65 'out_cm/output.${gxy2omsext("consensusxml")}'
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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66 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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68 -out_feat
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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69 ${' '.join(["'out_feat/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])}
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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70 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 #if $in_contaminants:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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72 -in_contaminants
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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74 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 #if $in_trafo:
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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76 -in_trafo
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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77 ${' '.join(["'in_trafo/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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78 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 | tee '$stdout'
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81 #end if
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82
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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83 ## Postprocessing
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84 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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85 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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86 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
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87 #end if
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88 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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89 ${' '.join(["&& mv -n 'in_postFDR/%(id)s.%(gext)s' 'out_feat/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out_feat if _])}
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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90 #end if
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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91 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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92 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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93 #end if]]></command>
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94 <configfiles>
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95 <inputs name="args_json" data_style="paths"/>
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96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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97 </configfiles>
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98 <inputs>
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99 <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
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100 <param name="in_raw" argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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101 <param name="in_postFDR" 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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102 <param name="in_contaminants" argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
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103 <param name="in_trafo" 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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104 <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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105 <param name="unit" argument="-FragmentMassError:unit" display="radio" type="select" optional="false" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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106 <option value="auto" selected="true">auto</option>
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107 <option value="ppm">ppm</option>
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108 <option value="da">da</option>
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109 <expand macro="list_string_san"/>
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110 </param>
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111 <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
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112 </section>
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113 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
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114 <param name="force_no_fdr" argument="-MS2_id_rate:force_no_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run if FDR is missing (accepts all pep_ids as target hits)" help=""/>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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115 </section>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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116 <expand macro="adv_opts_macro">
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117 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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118 <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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119 <expand macro="list_string_san"/>
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120 </param>
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121 </expand>
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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122 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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123 <option value="out_cm_FLAG">out_cm (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option>
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124 <option value="out_feat_FLAG">out_feat (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option>
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125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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126 </param>
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127 </inputs>
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128 <outputs>
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129 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
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130 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
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131 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
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132 </data>
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133 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
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134 <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
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135 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
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136 </collection>
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137 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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138 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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139 </data>
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140 </outputs>
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141 <tests>
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142 <expand macro="autotest_QualityControl"/>
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143 <expand macro="manutest_QualityControl"/>
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144 </tests>
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145 <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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146
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147
be0252d4f146 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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148 For more information, visit http://www.openms.de/documentation/TOPP_QualityControl.html]]></help>
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149 <expand macro="references"/>
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150 </tool>