annotate PeptideIndexer.xml @ 13:d6aca689dd48 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:11:03 +0000
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Refreshes the protein references for all peptide hits.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PeptideIndexer</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 #if $fasta:
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20 mkdir fasta &&
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21 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
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22 #end if
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23 mkdir out &&
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25 ## Main program call
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26
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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33 #if $fasta:
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34 -fasta
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35 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
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36 #end if
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37 -out
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38 'out/output.${gxy2omsext("idxml")}'
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39
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40 ## Postprocessing
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41 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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44 #end if]]></command>
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45 <configfiles>
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46 <inputs name="args_json" data_style="paths"/>
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <param argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
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51 <param argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
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52 <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
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53 <expand macro="list_string_san" name="decoy_string"/>
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54 </param>
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55 <param argument="-decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
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56 <option value="prefix" selected="true">prefix</option>
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57 <option value="suffix">suffix</option>
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58 <expand macro="list_string_san" name="decoy_string_position"/>
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59 </param>
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60 <param argument="-missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
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61 <option value="error" selected="true">error</option>
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62 <option value="warn">warn</option>
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63 <option value="silent">silent</option>
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64 <expand macro="list_string_san" name="missing_decoy_action"/>
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65 </param>
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66 <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
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67 <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
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68 <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
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69 <param argument="-unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
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70 <option value="error" selected="true">error</option>
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71 <option value="warn">warn</option>
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72 <option value="remove">remove</option>
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73 <expand macro="list_string_san" name="unmatched_action"/>
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74 </param>
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75 <param argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
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76 <param argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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77 <param argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
9
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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78 <section name="enzyme" title="" help="" expanded="false">
13
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diff changeset
79 <param name="name" argument="-enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
11
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80 <option value="auto" selected="true">auto</option>
13
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81 <option value="Arg-C">Arg-C</option>
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galaxyp
parents: 11
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82 <option value="Arg-C/P">Arg-C/P</option>
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83 <option value="Asp-N">Asp-N</option>
11
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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84 <option value="Asp-N/B">Asp-N/B</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 10
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85 <option value="Asp-N_ambic">Asp-N_ambic</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 10
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86 <option value="Chymotrypsin">Chymotrypsin</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 10
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87 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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88 <option value="CNBr">CNBr</option>
13
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galaxyp
parents: 11
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89 <option value="Formic_acid">Formic_acid</option>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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90 <option value="Lys-C">Lys-C</option>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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91 <option value="Lys-N">Lys-N</option>
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galaxyp
parents: 11
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92 <option value="Trypsin/P">Trypsin/P</option>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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93 <option value="V8-DE">V8-DE</option>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
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94 <option value="V8-E">V8-E</option>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
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95 <option value="leukocyte elastase">leukocyte elastase</option>
11
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96 <option value="proline endopeptidase">proline endopeptidase</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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97 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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98 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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99 <option value="2-iodobenzoate">2-iodobenzoate</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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100 <option value="iodosobenzoate">iodosobenzoate</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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101 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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102 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
9
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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103 <option value="Glu-C+P">Glu-C+P</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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104 <option value="PepsinA + P">PepsinA + P</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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105 <option value="cyanogen-bromide">cyanogen-bromide</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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106 <option value="Clostripain/P">Clostripain/P</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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107 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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108 <option value="no cleavage">no cleavage</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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109 <option value="unspecific cleavage">unspecific cleavage</option>
10
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galaxyp
parents: 9
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110 <option value="Lys-C/P">Lys-C/P</option>
13
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111 <option value="PepsinA">PepsinA</option>
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112 <option value="TrypChymo">TrypChymo</option>
11
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113 <option value="Trypsin">Trypsin</option>
13
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114 <expand macro="list_string_san" name="name"/>
9
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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115 </param>
13
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116 <param name="specificity" argument="-enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
11
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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117 <option value="auto" selected="true">auto</option>
d8ee5700c66b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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118 <option value="full">full</option>
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119 <option value="semi">semi</option>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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120 <option value="none">none</option>
13
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121 <expand macro="list_string_san" name="specificity"/>
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c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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122 </param>
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123 </section>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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124 <expand macro="adv_opts_macro">
13
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125 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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126 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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127 <expand macro="list_string_san" name="test"/>
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128 </param>
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129 </expand>
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130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
9
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131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0
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132 </param>
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133 </inputs>
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134 <outputs>
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135 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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138 </data>
0
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139 </outputs>
13
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140 <tests><!-- TOPP_PeptideIndexer_1 -->
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141 <test expect_num_outputs="2">
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142 <section name="adv_opts">
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143 <param name="force" value="false"/>
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144 <param name="test" value="true"/>
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145 </section>
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146 <param name="in" value="PeptideIndexer_1.idXML"/>
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147 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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148 <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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149 <param name="decoy_string" value=""/>
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150 <param name="decoy_string_position" value="prefix"/>
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151 <param name="missing_decoy_action" value="error"/>
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152 <param name="write_protein_sequence" value="false"/>
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153 <param name="write_protein_description" value="false"/>
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154 <param name="keep_unreferenced_proteins" value="false"/>
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155 <param name="unmatched_action" value="warn"/>
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156 <param name="aaa_max" value="4"/>
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157 <param name="mismatches_max" value="0"/>
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158 <param name="IL_equivalent" value="false"/>
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159 <section name="enzyme">
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160 <param name="name" value="auto"/>
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161 <param name="specificity" value="none"/>
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162 </section>
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163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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164 <output name="ctd_out" ftype="xml">
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165 <assert_contents>
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166 <is_valid_xml/>
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167 </assert_contents>
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168 </output>
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169 </test>
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170 <!-- TOPP_PeptideIndexer_2 -->
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171 <test expect_num_outputs="2">
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172 <section name="adv_opts">
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173 <param name="force" value="false"/>
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174 <param name="test" value="true"/>
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175 </section>
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176 <param name="in" value="PeptideIndexer_1.idXML"/>
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177 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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178 <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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179 <param name="decoy_string" value=""/>
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180 <param name="decoy_string_position" value="prefix"/>
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181 <param name="missing_decoy_action" value="error"/>
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182 <param name="write_protein_sequence" value="true"/>
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183 <param name="write_protein_description" value="false"/>
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184 <param name="keep_unreferenced_proteins" value="false"/>
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185 <param name="unmatched_action" value="warn"/>
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186 <param name="aaa_max" value="4"/>
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187 <param name="mismatches_max" value="0"/>
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188 <param name="IL_equivalent" value="false"/>
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189 <section name="enzyme">
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190 <param name="name" value="auto"/>
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191 <param name="specificity" value="none"/>
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192 </section>
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193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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194 <output name="ctd_out" ftype="xml">
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195 <assert_contents>
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196 <is_valid_xml/>
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197 </assert_contents>
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198 </output>
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199 </test>
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200 <!-- TOPP_PeptideIndexer_3 -->
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201 <test expect_num_outputs="2">
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202 <section name="adv_opts">
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203 <param name="force" value="false"/>
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204 <param name="test" value="true"/>
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205 </section>
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206 <param name="in" value="PeptideIndexer_1.idXML"/>
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207 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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208 <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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209 <param name="decoy_string" value=""/>
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210 <param name="decoy_string_position" value="prefix"/>
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211 <param name="missing_decoy_action" value="error"/>
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212 <param name="write_protein_sequence" value="false"/>
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213 <param name="write_protein_description" value="false"/>
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214 <param name="keep_unreferenced_proteins" value="true"/>
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215 <param name="unmatched_action" value="warn"/>
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216 <param name="aaa_max" value="4"/>
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217 <param name="mismatches_max" value="0"/>
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218 <param name="IL_equivalent" value="false"/>
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219 <section name="enzyme">
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220 <param name="name" value="auto"/>
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221 <param name="specificity" value="none"/>
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222 </section>
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223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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224 <output name="ctd_out" ftype="xml">
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225 <assert_contents>
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226 <is_valid_xml/>
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227 </assert_contents>
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228 </output>
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229 </test>
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230 <!-- TOPP_PeptideIndexer_4 -->
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231 <test expect_num_outputs="2">
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232 <section name="adv_opts">
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233 <param name="force" value="false"/>
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234 <param name="test" value="true"/>
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235 </section>
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236 <param name="in" value="PeptideIndexer_1.idXML"/>
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237 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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238 <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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239 <param name="decoy_string" value=""/>
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240 <param name="decoy_string_position" value="prefix"/>
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241 <param name="missing_decoy_action" value="error"/>
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242 <param name="write_protein_sequence" value="true"/>
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243 <param name="write_protein_description" value="false"/>
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244 <param name="keep_unreferenced_proteins" value="false"/>
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245 <param name="unmatched_action" value="warn"/>
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246 <param name="aaa_max" value="0"/>
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247 <param name="mismatches_max" value="0"/>
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248 <param name="IL_equivalent" value="false"/>
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249 <section name="enzyme">
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250 <param name="name" value="auto"/>
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251 <param name="specificity" value="none"/>
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252 </section>
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253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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254 <output name="ctd_out" ftype="xml">
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255 <assert_contents>
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256 <is_valid_xml/>
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257 </assert_contents>
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258 </output>
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259 </test>
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260 <!-- TOPP_PeptideIndexer_5 -->
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261 <test expect_num_outputs="2">
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262 <section name="adv_opts">
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263 <param name="force" value="false"/>
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264 <param name="test" value="true"/>
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265 </section>
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266 <param name="in" value="PeptideIndexer_1.idXML"/>
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267 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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268 <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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269 <param name="decoy_string" value=""/>
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270 <param name="decoy_string_position" value="prefix"/>
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271 <param name="missing_decoy_action" value="error"/>
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272 <param name="write_protein_sequence" value="false"/>
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273 <param name="write_protein_description" value="false"/>
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274 <param name="keep_unreferenced_proteins" value="false"/>
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275 <param name="unmatched_action" value="warn"/>
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276 <param name="aaa_max" value="4"/>
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277 <param name="mismatches_max" value="0"/>
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278 <param name="IL_equivalent" value="false"/>
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279 <section name="enzyme">
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280 <param name="name" value="auto"/>
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281 <param name="specificity" value="none"/>
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282 </section>
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283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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284 <output name="ctd_out" ftype="xml">
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285 <assert_contents>
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286 <is_valid_xml/>
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287 </assert_contents>
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288 </output>
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289 </test>
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290 <!-- TOPP_PeptideIndexer_6 -->
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291 <test expect_num_outputs="2">
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292 <section name="adv_opts">
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293 <param name="force" value="false"/>
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294 <param name="test" value="true"/>
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295 </section>
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296 <param name="in" value="PeptideIndexer_2.idXML"/>
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297 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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298 <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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299 <param name="decoy_string" value=""/>
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300 <param name="decoy_string_position" value="prefix"/>
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301 <param name="missing_decoy_action" value="error"/>
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302 <param name="write_protein_sequence" value="false"/>
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303 <param name="write_protein_description" value="false"/>
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304 <param name="keep_unreferenced_proteins" value="false"/>
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305 <param name="unmatched_action" value="warn"/>
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306 <param name="aaa_max" value="3"/>
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307 <param name="mismatches_max" value="0"/>
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308 <param name="IL_equivalent" value="false"/>
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309 <section name="enzyme">
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310 <param name="name" value="auto"/>
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311 <param name="specificity" value="none"/>
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312 </section>
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313 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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314 <output name="ctd_out" ftype="xml">
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315 <assert_contents>
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316 <is_valid_xml/>
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317 </assert_contents>
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318 </output>
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319 </test>
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320 <!-- TOPP_PeptideIndexer_7 -->
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321 <test expect_num_outputs="2">
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322 <section name="adv_opts">
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323 <param name="force" value="false"/>
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324 <param name="test" value="true"/>
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325 </section>
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326 <param name="in" value="PeptideIndexer_3.idXML"/>
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galaxyp
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327 <param name="fasta" value="PeptideIndexer_1.fasta"/>
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328 <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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galaxyp
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329 <param name="decoy_string" value="DECOY_"/>
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galaxyp
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330 <param name="decoy_string_position" value="prefix"/>
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galaxyp
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331 <param name="missing_decoy_action" value="error"/>
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galaxyp
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332 <param name="write_protein_sequence" value="false"/>
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galaxyp
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333 <param name="write_protein_description" value="false"/>
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galaxyp
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334 <param name="keep_unreferenced_proteins" value="false"/>
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galaxyp
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335 <param name="unmatched_action" value="warn"/>
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galaxyp
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336 <param name="aaa_max" value="4"/>
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galaxyp
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337 <param name="mismatches_max" value="0"/>
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galaxyp
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338 <param name="IL_equivalent" value="false"/>
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galaxyp
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339 <section name="enzyme">
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galaxyp
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340 <param name="name" value="auto"/>
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galaxyp
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341 <param name="specificity" value="full"/>
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342 </section>
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galaxyp
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343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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galaxyp
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344 <output name="ctd_out" ftype="xml">
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galaxyp
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345 <assert_contents>
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galaxyp
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346 <is_valid_xml/>
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galaxyp
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347 </assert_contents>
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348 </output>
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349 </test>
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galaxyp
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350 <!-- TOPP_PeptideIndexer_8 -->
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galaxyp
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351 <test expect_num_outputs="2">
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galaxyp
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352 <section name="adv_opts">
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galaxyp
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353 <param name="force" value="false"/>
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galaxyp
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354 <param name="test" value="true"/>
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galaxyp
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355 </section>
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galaxyp
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356 <param name="in" value="PeptideIndexer_3.idXML"/>
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galaxyp
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357 <param name="fasta" value="PeptideIndexer_1.fasta"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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galaxyp
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359 <param name="decoy_string" value=""/>
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galaxyp
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360 <param name="decoy_string_position" value="prefix"/>
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galaxyp
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361 <param name="missing_decoy_action" value="error"/>
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galaxyp
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362 <param name="write_protein_sequence" value="false"/>
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galaxyp
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363 <param name="write_protein_description" value="false"/>
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galaxyp
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364 <param name="keep_unreferenced_proteins" value="false"/>
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galaxyp
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365 <param name="unmatched_action" value="warn"/>
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galaxyp
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366 <param name="aaa_max" value="4"/>
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galaxyp
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367 <param name="mismatches_max" value="0"/>
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galaxyp
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368 <param name="IL_equivalent" value="false"/>
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galaxyp
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369 <section name="enzyme">
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galaxyp
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370 <param name="name" value="auto"/>
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galaxyp
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371 <param name="specificity" value="semi"/>
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galaxyp
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372 </section>
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galaxyp
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373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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galaxyp
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374 <output name="ctd_out" ftype="xml">
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galaxyp
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375 <assert_contents>
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galaxyp
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376 <is_valid_xml/>
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galaxyp
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377 </assert_contents>
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galaxyp
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378 </output>
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galaxyp
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379 </test>
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galaxyp
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380 <!-- TOPP_PeptideIndexer_9 -->
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galaxyp
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381 <test expect_num_outputs="2">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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382 <section name="adv_opts">
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galaxyp
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383 <param name="force" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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384 <param name="test" value="true"/>
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galaxyp
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385 </section>
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galaxyp
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diff changeset
386 <param name="in" value="PeptideIndexer_3.idXML"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
387 <param name="fasta" value="PeptideIndexer_1.fasta"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
388 <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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galaxyp
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diff changeset
389 <param name="decoy_string" value=""/>
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galaxyp
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diff changeset
390 <param name="decoy_string_position" value="prefix"/>
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galaxyp
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391 <param name="missing_decoy_action" value="error"/>
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galaxyp
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392 <param name="write_protein_sequence" value="false"/>
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galaxyp
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393 <param name="write_protein_description" value="false"/>
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galaxyp
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394 <param name="keep_unreferenced_proteins" value="false"/>
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galaxyp
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diff changeset
395 <param name="unmatched_action" value="remove"/>
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galaxyp
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396 <param name="aaa_max" value="4"/>
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galaxyp
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397 <param name="mismatches_max" value="0"/>
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galaxyp
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398 <param name="IL_equivalent" value="false"/>
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galaxyp
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399 <section name="enzyme">
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galaxyp
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400 <param name="name" value="auto"/>
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401 <param name="specificity" value="none"/>
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402 </section>
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galaxyp
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diff changeset
403 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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galaxyp
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404 <output name="ctd_out" ftype="xml">
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galaxyp
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405 <assert_contents>
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galaxyp
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406 <is_valid_xml/>
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galaxyp
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407 </assert_contents>
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galaxyp
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408 </output>
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galaxyp
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409 </test>
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galaxyp
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diff changeset
410 <!-- TOPP_PeptideIndexer_10 -->
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galaxyp
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diff changeset
411 <test expect_num_outputs="2">
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parents: 11
diff changeset
412 <section name="adv_opts">
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galaxyp
parents: 11
diff changeset
413 <param name="force" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
414 <param name="test" value="true"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
415 </section>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
416 <param name="in" value="PeptideIndexer_10_input.idXML"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
417 <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
418 <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
419 <param name="decoy_string" value=""/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
420 <param name="decoy_string_position" value="prefix"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
421 <param name="missing_decoy_action" value="error"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
422 <param name="write_protein_sequence" value="true"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
423 <param name="write_protein_description" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
424 <param name="keep_unreferenced_proteins" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
425 <param name="unmatched_action" value="error"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
426 <param name="aaa_max" value="3"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
427 <param name="mismatches_max" value="0"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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428 <param name="IL_equivalent" value="true"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
429 <section name="enzyme">
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galaxyp
parents: 11
diff changeset
430 <param name="name" value="auto"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
431 <param name="specificity" value="auto"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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432 </section>
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galaxyp
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diff changeset
433 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
434 <output name="ctd_out" ftype="xml">
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galaxyp
parents: 11
diff changeset
435 <assert_contents>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
436 <is_valid_xml/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
437 </assert_contents>
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galaxyp
parents: 11
diff changeset
438 </output>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
439 </test>
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galaxyp
parents: 11
diff changeset
440 <!-- TOPP_PeptideIndexer_12 -->
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galaxyp
parents: 11
diff changeset
441 <test expect_num_outputs="2">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
442 <section name="adv_opts">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
443 <param name="force" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
444 <param name="test" value="true"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
445 </section>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
446 <param name="in" value="PeptideIndexer_1.idXML"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
447 <param name="fasta" value="PeptideIndexer_1.fasta"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
448 <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
449 <param name="decoy_string" value=""/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
450 <param name="decoy_string_position" value="prefix"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
451 <param name="missing_decoy_action" value="error"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
452 <param name="write_protein_sequence" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
453 <param name="write_protein_description" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
454 <param name="keep_unreferenced_proteins" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
455 <param name="unmatched_action" value="warn"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
456 <param name="aaa_max" value="4"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
457 <param name="mismatches_max" value="0"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
458 <param name="IL_equivalent" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
459 <section name="enzyme">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
460 <param name="name" value="auto"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
461 <param name="specificity" value="none"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
462 </section>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
463 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
464 <output name="ctd_out" ftype="xml">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
465 <assert_contents>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
466 <is_valid_xml/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
467 </assert_contents>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
468 </output>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
469 </test>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
470 <!-- TOPP_PeptideIndexer_13 -->
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
471 <test expect_num_outputs="2">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
472 <section name="adv_opts">
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
473 <param name="force" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
474 <param name="test" value="true"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
475 </section>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
476 <param name="in" value="empty.idXML"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
477 <param name="fasta" value="PeptideIndexer_1.fasta"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
478 <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
479 <param name="decoy_string" value=""/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
480 <param name="decoy_string_position" value="prefix"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
481 <param name="missing_decoy_action" value="error"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
482 <param name="write_protein_sequence" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
483 <param name="write_protein_description" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
484 <param name="keep_unreferenced_proteins" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
485 <param name="unmatched_action" value="error"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
486 <param name="aaa_max" value="4"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
487 <param name="mismatches_max" value="0"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
488 <param name="IL_equivalent" value="false"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
489 <section name="enzyme">
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galaxyp
parents: 11
diff changeset
490 <param name="name" value="auto"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
491 <param name="specificity" value="auto"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
492 </section>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
494 <output name="ctd_out" ftype="xml">
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galaxyp
parents: 11
diff changeset
495 <assert_contents>
d6aca689dd48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
496 <is_valid_xml/>
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galaxyp
parents: 11
diff changeset
497 </assert_contents>
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galaxyp
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498 </output>
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499 </test>
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500 <!-- TOPP_PeptideIndexer_14 -->
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501 <test expect_num_outputs="2">
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502 <section name="adv_opts">
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503 <param name="force" value="false"/>
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504 <param name="test" value="true"/>
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505 </section>
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506 <param name="in" value="PeptideIndexer_14.idXML"/>
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507 <param name="fasta" value="PeptideIndexer_2.fasta"/>
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508 <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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509 <param name="decoy_string" value=""/>
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510 <param name="decoy_string_position" value="prefix"/>
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511 <param name="missing_decoy_action" value="error"/>
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512 <param name="write_protein_sequence" value="true"/>
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513 <param name="write_protein_description" value="false"/>
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514 <param name="keep_unreferenced_proteins" value="false"/>
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515 <param name="unmatched_action" value="error"/>
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516 <param name="aaa_max" value="4"/>
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517 <param name="mismatches_max" value="0"/>
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518 <param name="IL_equivalent" value="false"/>
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519 <section name="enzyme">
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520 <param name="name" value="auto"/>
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521 <param name="specificity" value="none"/>
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522 </section>
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523 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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524 <output name="ctd_out" ftype="xml">
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525 <assert_contents>
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526 <is_valid_xml/>
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527 </assert_contents>
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528 </output>
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529 </test>
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c4a73c6a8dca "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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530 </tests>
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531 <help><![CDATA[Refreshes the protein references for all peptide hits.
0
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532
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533
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534 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help>
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535 <expand macro="references"/>
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536 </tool>