Mercurial > repos > galaxyp > openms_idmerger

annotate IDMerger.xml @ 13:978de6b97ca8 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 19:52:43 +0000
parents 64dbb1eb0048
children 34e7afee141d
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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: [File Handling]-->
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4 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Merges several protein/peptide identification files into one file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMerger</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 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir out &&
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22 #if $add_to:
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23 mkdir add_to &&
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24 ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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35 -out
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36 'out/output.${gxy2omsext("idxml")}'
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37 #if $add_to:
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38 -add_to
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39 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)'
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40 #end if
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41
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42 ## Postprocessing
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43 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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46 #end if]]></command>
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47 <configfiles>
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48 <inputs name="args_json" data_style="paths"/>
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49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="Input files separated by blanks" help=" select idxml data sets(s)"/>
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53 <param name="add_to" argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/>
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54 <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help=""/>
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55 <param name="pepxml_protxml" argument="-pepxml_protxml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
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56 <param name="merge_proteins_add_PSMs" argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
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57 <expand macro="adv_opts_macro">
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58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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59 <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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60 <expand macro="list_string_san"/>
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61 </param>
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62 </expand>
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63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <expand macro="autotest_IDMerger"/>
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75 <expand macro="manutest_IDMerger"/>
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76 </tests>
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77 <help><![CDATA[Merges several protein/peptide identification files into one file.
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79
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80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDMerger.html]]></help>
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64dbb1eb0048 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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81 <expand macro="references"/>
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75805008dd71 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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82 </tool>