Mercurial > repos > galaxyp > openms_idconflictresolver

annotate IDConflictResolver.xml @ 16:98570407f418 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 19:19:11 +0000
parents 1b6e681b91f6
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1ddb1b5968a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Resolves ambiguous annotations of features with peptide identifications</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDConflictResolver</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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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($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${in.ext}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${in.ext}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
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45 <param name="resolve_between_features" argument="-resolve_between_features" display="radio" type="select" optional="false" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
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46 <option value="off" selected="true">off</option>
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47 <option value="highest_intensity">highest_intensity</option>
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48 <expand macro="list_string_san"/>
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49 </param>
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50 <expand macro="adv_opts_macro">
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51 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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52 <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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53 <expand macro="list_string_san"/>
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54 </param>
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55 </expand>
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56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <expand macro="autotest_IDConflictResolver"/>
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68 <expand macro="manutest_IDConflictResolver"/>
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69 </tests>
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70 <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications
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72
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73 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDConflictResolver.html]]></help>
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74 <expand macro="references"/>
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75 </tool>