Mercurial > repos > galaxyp > openms_maraclusteradapter

annotate MaRaClusterAdapter.xml @ 4:f7195ee7e18d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:16 +0000
parents 2be8c63444db
children
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c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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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]-->
4
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4 <tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Facilitate input to MaRaCluster and reintegrate.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MaRaClusterAdapter</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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15
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 ## Preprocessing
4
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17 mkdir in_cond.in &&
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18 #if $in_cond.in_select == "no"
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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21 #else
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
f7195ee7e18d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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23 #end if
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24 #if $id_in_cond.id_in:
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25 mkdir id_in_cond.id_in &&
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26 #if $id_in_cond.id_in_select == "no"
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27 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} &&
f7195ee7e18d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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28 ${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
f7195ee7e18d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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29 #else
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30 ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
f7195ee7e18d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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31 #end if
0
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32 #end if
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33 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir out &&
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35 #end if
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36
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37 ## Main program call
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38
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 -in
4
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44 #if $in_cond.in_select == "no"
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45 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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46 #else
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47 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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48 #end if
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49 #if $id_in_cond.id_in:
0
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50 -id_in
4
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51 #if $id_in_cond.id_in_select == "no"
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52 ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
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53 #else
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54 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
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55 #end if
0
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56 #end if
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57 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 -out
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59 'out/output.${gxy2omsext("idxml")}'
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60 #end if
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61 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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62 | tee '$stdout'
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63 #end if
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64
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65 ## Postprocessing
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66 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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67 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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68 #end if
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69 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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70 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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71 #end if]]></command>
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72 <configfiles>
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73 <inputs name="args_json" data_style="paths"/>
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74 <configfile name="hardcoded_json"><![CDATA[{"maracluster_executable": "/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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75 </configfiles>
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76 <inputs>
4
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77 <conditional name="in_cond">
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78 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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79 <option value="no">No: process all datasets jointly</option>
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80 <option value="yes">Yes: process each dataset in an independent job</option>
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81 </param>
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82 <when value="no">
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83 <param argument="-in" type="data" format="mgf,mzml" multiple="true" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
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84 </when>
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85 <when value="yes">
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86 <param argument="-in" type="data" format="mgf,mzml" multiple="false" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
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87 </when>
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88 </conditional>
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89 <conditional name="id_in_cond">
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90 <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
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91 <option value="no">No: process all datasets jointly</option>
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92 <option value="yes">Yes: process each dataset in an independent job</option>
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93 </param>
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94 <when value="no">
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95 <param argument="-id_in" type="data" format="idxml" multiple="true" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
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96 </when>
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97 <when value="yes">
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98 <param argument="-id_in" type="data" format="idxml" multiple="false" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
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99 </when>
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100 </conditional>
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101 <param argument="-pcut" type="float" optional="true" max="0.0" value="-10.0" label="log(p-value) cutoff, has to be &lt; 0.0" help="Default: -10.0"/>
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102 <param argument="-min_cluster_size" type="integer" optional="true" min="1" value="1" label="minimum number of spectra in a cluster for consensus spectra" help=""/>
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103 <expand macro="adv_opts_macro">
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104 <param argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
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105 <param argument="-precursor_tolerance" type="float" optional="true" value="20.0" label="Precursor monoisotopic mass tolerance" help=""/>
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106 <param argument="-precursor_tolerance_units" type="select" optional="true" label="tolerance_mass_units 0=ppm, 1=Da" help="">
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107 <option value="ppm" selected="true">ppm</option>
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108 <option value="Da">Da</option>
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109 <expand macro="list_string_san" name="precursor_tolerance_units"/>
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110 </param>
4
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111 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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112 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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113 <expand macro="list_string_san" name="test"/>
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114 </param>
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115 </expand>
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116 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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117 <option value="out_FLAG">out (Output file in idXML format)</option>
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118 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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119 </param>
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120 </inputs>
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121 <outputs>
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122 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
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123 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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124 </data>
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125 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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126 <filter>OPTIONAL_OUTPUTS is None</filter>
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127 </data>
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128 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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129 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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130 </data>
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131 </outputs>
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132 <tests><!-- TOPP_MaRaClusterAdapter_2 -->
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133 </tests>
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134 <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
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135
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136
4
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137 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MaRaClusterAdapter.html]]></help>
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138 <expand macro="references"/>
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139 </tool>