Mercurial > repos > galaxyp > openms_proteinquantifier

annotate ProteinQuantifier.xml @ 10:8a45fd5a608a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 11:58:12 +0000
parents f874f2998576
children bb1e75938909
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7652a9664052 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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fbae1b1acf70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Quantitation]-->
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4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Compute peptide and protein abundances</description>
7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinQuantifier</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
f874f2998576 "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>
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 </macros>
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12 <expand macro="requirements"/>
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 <expand macro="stdio"/>
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f874f2998576 "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@
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 @EXT_FOO@
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 #import re
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17
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18 ## Preprocessing
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 mkdir in &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 #if $protein_groups:
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22 mkdir protein_groups &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
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24 #end if
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25 #if $design:
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 mkdir design &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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28 #end if
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29 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 mkdir out &&
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 #end if
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32 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 mkdir peptide_out &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 #end if
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 mkdir mztab &&
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37 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 ## Main program call
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 set -o pipefail &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 @EXECUTABLE@ -write_ctd ./ &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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45 -in
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46 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 #if $protein_groups:
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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48 -protein_groups
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)'
0
7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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50 #end if
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51 #if $design:
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52 -design
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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53 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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54 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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55 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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56 -out
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57 'out/output.${gxy2omsext("csv")}'
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58 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 -peptide_out
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 'peptide_out/output.${gxy2omsext("csv")}'
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62 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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64 -mztab
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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65 'mztab/output.${gxy2omsext("mztab")}'
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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66 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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68 | tee '$stdout'
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69 #end if
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70
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 ## Postprocessing
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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72 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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7652a9664052 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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74 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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76 && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out'
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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77 #end if
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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78 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab'
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80 #end if
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f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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82 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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83 #end if]]></command>
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84 <configfiles>
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85 <inputs name="args_json" data_style="paths"/>
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86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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87 </configfiles>
0
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88 <inputs>
9
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89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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90 <param name="protein_groups" argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
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91 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
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92 <param name="top" argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
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93 <param name="average" argument="-average" display="radio" type="select" optional="false" label="Averaging method used to compute protein abundances from peptide abundances" help="">
0
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94 <option value="median" selected="true">median</option>
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95 <option value="mean">mean</option>
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96 <option value="weighted_mean">weighted_mean</option>
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97 <option value="sum">sum</option>
9
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98 <expand macro="list_string_san"/>
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99 </param>
9
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100 <param name="include_all" argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
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101 <param name="best_charge_and_fraction" argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
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102 <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
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103 <param name="ratios" argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
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104 <param name="ratiosSILAC" argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
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105 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
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106 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
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107 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0', all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
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108 </section>
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109 <section name="format" title="Output formatting options" help="" expanded="false">
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110 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
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111 <expand macro="list_string_san"/>
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112 </param>
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113 <param name="quoting" argument="-format:quoting" display="radio" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
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114 <option value="none">none</option>
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115 <option value="double" selected="true">double</option>
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116 <option value="escape">escape</option>
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117 <expand macro="list_string_san"/>
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118 </param>
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119 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
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120 <expand macro="list_string_san"/>
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121 </param>
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122 </section>
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123 <expand macro="adv_opts_macro">
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124 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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125 <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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126 <expand macro="list_string_san"/>
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127 </param>
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128 </expand>
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129 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
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130 <option value="out_FLAG">out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
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131 <option value="peptide_out_FLAG">peptide_out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
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132 <option value="mztab_FLAG">mztab (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
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133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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134 </param>
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135 </inputs>
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136 <outputs>
9
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137 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
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138 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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139 </data>
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140 <data name="peptide_out" label="${tool.name} on ${on_string}: peptide_out" format="csv">
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141 <filter>OPTIONAL_OUTPUTS is not None and "peptide_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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142 </data>
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143 <data name="mztab" label="${tool.name} on ${on_string}: mztab" format="mztab">
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144 <filter>OPTIONAL_OUTPUTS is not None and "mztab_FLAG" in OPTIONAL_OUTPUTS</filter>
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145 </data>
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146 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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147 <filter>OPTIONAL_OUTPUTS is None</filter>
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148 </data>
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149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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151 </data>
0
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152 </outputs>
9
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153 <tests>
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154 <expand macro="autotest_ProteinQuantifier"/>
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155 <expand macro="manutest_ProteinQuantifier"/>
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156 </tests>
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157 <help><![CDATA[Compute peptide and protein abundances
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159
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160 For more information, visit http://www.openms.de/documentation/TOPP_ProteinQuantifier.html]]></help>
f874f2998576 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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161 <expand macro="references"/>
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162 </tool>