Mercurial > repos > galaxyp > openms_gnpsexport

annotate GNPSExport.xml @ 0:22885d201eb8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 13:01:50 +0000
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children 2dabae2814df
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22885d201eb8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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: []-->
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4 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Tool to export consensus features into MGF format</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">GNPSExport</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_cm &&
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20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
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21 mkdir in_mzml &&
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22 ${ ' '.join(["ln -s '%s' 'in_mzml/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _]) }
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23 mkdir out &&
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24
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25 ## Main program call
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26
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__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_cm
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32 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
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33 -in_mzml
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34 ${' '.join(["'in_mzml/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])}
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35 -out
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36 'out/output.${gxy2omsext("mgf")}'
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37
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38 ## Postprocessing
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39 && mv 'out/output.${gxy2omsext("mgf")}' '$out'
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40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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42 #end if]]></command>
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43 <configfiles>
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44 <inputs name="args_json" data_style="paths"/>
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45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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46 </configfiles>
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47 <inputs>
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48 <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="input file containing consensus elements with 'peptide' annotations" help=" select consensusxml data sets(s)"/>
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49 <param name="in_mzml" argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="original mzml files containing ms/ms spectrum information" help=" select mzml data sets(s)"/>
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50 <param name="output_type" argument="-output_type" display="radio" type="select" optional="false" label="specificity of mgf output information" help="">
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51 <option value="full_spectra" selected="true">full_spectra</option>
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52 <option value="merged_spectra">merged_spectra</option>
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53 <expand macro="list_string_san"/>
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54 </param>
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55 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" value="0.0001" label="Tolerance mz window for precursor selection" help=""/>
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56 <param name="precursor_rt_tolerance" argument="-precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance rt window for precursor selection" help=""/>
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57 <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per feature" help="" expanded="false">
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58 <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" value="0.95" label="Cosine similarity threshold for merged_spectra output" help=""/>
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59 </section>
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60 <expand macro="adv_opts_macro">
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61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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62 <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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63 <expand macro="list_string_san"/>
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64 </param>
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65 </expand>
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66 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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68 </param>
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69 </inputs>
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70 <outputs>
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71 <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/>
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72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <expand macro="autotest_GNPSExport"/>
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78 <expand macro="manutest_GNPSExport"/>
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79 </tests>
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80 <help><![CDATA[Tool to export consensus features into MGF format
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81
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82 ]]></help>
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83 <expand macro="references"/>
22885d201eb8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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84 </tool>