Mercurial > repos > galaxyp > openms_erpairfinder

annotate ERPairFinder.xml @ 13:e5e2b0d57f1d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:24:38 +0000
parents 919d5280d1db
children d6ef464ff66b
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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="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ERPairFinder</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($in.ext)' &&
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21 mkdir pair_in &&
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22 ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
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23 mkdir out &&
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24 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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25 mkdir feature_out &&
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26 #end if
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28 ## Main program call
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30 set -o pipefail &&
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31 @EXECUTABLE@ -write_ctd ./ &&
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32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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34 -in
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35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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36 -pair_in
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37 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)'
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38 -out
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39 'out/output.${gxy2omsext("consensusxml")}'
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40 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 -feature_out
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42 'feature_out/output.${gxy2omsext("featurexml")}'
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43 #end if
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44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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45 | tee '$stdout'
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46 #end if
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48 ## Postprocessing
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49 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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50 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 && mv 'feature_out/output.${gxy2omsext("featurexml")}' '$feature_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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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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="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
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62 <param name="pair_in" argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
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63 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
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64 <expand macro="adv_opts_macro">
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65 <param name="RT_tolerance" argument="-RT_tolerance" type="float" optional="true" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
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66 <param name="max_charge" argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
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67 <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
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68 <param name="max_isotope" argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
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69 <param name="expansion_range" argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
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70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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71 <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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72 <expand macro="list_string_san"/>
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73 </param>
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74 </expand>
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75 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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76 <option value="feature_out_FLAG">feature_out (Output featureXML file, only written if given, skipped otherwise)</option>
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77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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78 </param>
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79 </inputs>
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80 <outputs>
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81 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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82 <data name="feature_out" label="${tool.name} on ${on_string}: feature_out" format="featurexml">
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83 <filter>OPTIONAL_OUTPUTS is not None and "feature_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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84 </data>
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85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <expand macro="autotest_ERPairFinder"/>
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91 <expand macro="manutest_ERPairFinder"/>
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92 </tests>
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93 <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
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94
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95
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96 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ERPairFinder.html]]></help>
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97 <expand macro="references"/>
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98 </tool>