Mercurial > repos > galaxyp > openms_maraclusteradapter

annotate MaRaClusterAdapter.xml @ 0:c1f58afbc706 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:17:43 +0000
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children 2be8c63444db
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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]-->
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4 <tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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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
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ## Preprocessing
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 #if $id_in:
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22 mkdir id_in &&
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23 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 #end if
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25 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 mkdir out &&
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27 #end if
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28
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 ## Main program call
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30
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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37 #if $id_in:
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38 -id_in
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39 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 #end if
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41 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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42 -out
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43 'out/output.${gxy2omsext("idxml")}'
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44 #end if
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45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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46 | tee '$stdout'
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47 #end if
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48
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49 ## Postprocessing
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50 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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52 #end if
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53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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55 #end if]]></command>
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56 <configfiles>
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57 <inputs name="args_json" data_style="paths"/>
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58 <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>
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 </configfiles>
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60 <inputs>
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61 <param name="in" 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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62 <param name="id_in" 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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63 <param name="pcut" 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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64 <param name="min_cluster_size" 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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65 <expand macro="adv_opts_macro">
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66 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
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67 <param name="precursor_tolerance" argument="-precursor_tolerance" type="float" optional="true" value="20.0" label="Precursor monoisotopic mass tolerance" help=""/>
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68 <param name="precursor_tolerance_units" argument="-precursor_tolerance_units" display="radio" type="select" optional="false" label="tolerance_mass_units 0=ppm, 1=Da" help="">
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69 <option value="ppm" selected="true">ppm</option>
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70 <option value="Da">Da</option>
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71 <expand macro="list_string_san"/>
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72 </param>
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73 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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74 <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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75 <expand macro="list_string_san"/>
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76 </param>
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77 </expand>
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78 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
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79 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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81 </param>
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82 </inputs>
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83 <outputs>
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84 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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85 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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86 </data>
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87 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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88 <filter>OPTIONAL_OUTPUTS is None</filter>
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89 </data>
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90 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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91 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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92 </data>
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93 </outputs>
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94 <tests>
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95 <expand macro="autotest_MaRaClusterAdapter"/>
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96 <expand macro="manutest_MaRaClusterAdapter"/>
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97 </tests>
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98 <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
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99
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100
c1f58afbc706 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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101 For more information, visit http://www.openms.de/documentation/TOPP_MaRaClusterAdapter.html]]></help>
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102 <expand macro="references"/>
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103 </tool>