Mercurial > repos > galaxyp > openms_multiplexresolver

annotate MultiplexResolver.xml @ 16:a56b0c3aa0dc draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 19:17:01 +0000
parents a319d00dc637
children
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c8871ea9a7b7 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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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Completes peptide multiplets and resolves conflicts within them.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MultiplexResolver</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 #if $in_blacklist:
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22 mkdir in_blacklist &&
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23 ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
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24 #end if
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25 mkdir out &&
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26 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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27 mkdir out_conflicts &&
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 -in
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37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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38 #if $in_blacklist:
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39 -in_blacklist
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40 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)'
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41 #end if
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42 -out
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43 'out/output.${gxy2omsext("consensusxml")}'
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44 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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45 -out_conflicts
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46 'out_conflicts/output.${gxy2omsext("consensusxml")}'
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47 #end if
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48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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49 | tee '$stdout'
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50 #end if
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51
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52 ## Postprocessing
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53 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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54 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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55 && mv 'out_conflicts/output.${gxy2omsext("consensusxml")}' '$out_conflicts'
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56 #end if
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57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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58 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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59 #end if]]></command>
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60 <configfiles>
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61 <inputs name="args_json" data_style="paths"/>
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62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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63 </configfiles>
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64 <inputs>
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65 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
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66 <param name="in_blacklist" argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
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67 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
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68 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. . [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
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69 <expand macro="list_string_san"/>
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70 </param>
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71 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
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72 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
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73 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
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74 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
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75 </section>
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76 <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false">
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77 <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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78 <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
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79 <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
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80 <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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81 <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
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82 <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
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83 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
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84 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
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85 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
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86 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
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87 <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
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88 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
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89 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
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90 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
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91 </section>
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92 <expand macro="adv_opts_macro">
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93 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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94 <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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95 <expand macro="list_string_san"/>
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96 </param>
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97 </expand>
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98 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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99 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option>
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100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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101 </param>
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102 </inputs>
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103 <outputs>
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104 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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105 <data name="out_conflicts" label="${tool.name} on ${on_string}: out_conflicts" format="consensusxml">
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106 <filter>OPTIONAL_OUTPUTS is not None and "out_conflicts_FLAG" in OPTIONAL_OUTPUTS</filter>
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107 </data>
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108 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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109 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <expand macro="autotest_MultiplexResolver"/>
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114 <expand macro="manutest_MultiplexResolver"/>
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115 </tests>
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116 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
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117
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118
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119 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MultiplexResolver.html]]></help>
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120 <expand macro="references"/>
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121 </tool>