annotate OpenSwathRewriteToFeatureXML.xml @ 9:175016416031 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:13:11 +0000
parents 63e463c4abc1
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</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 #if $csv:
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20 mkdir csv &&
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21 ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
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22 #end if
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23 mkdir featureXML &&
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24 ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
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25 mkdir out &&
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27 ## Main program call
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28
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__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 #if $csv:
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34 -csv
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35 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)'
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36 #end if
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37 -featureXML
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38 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)'
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39 -out
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40 'out/output.${gxy2omsext("featurexml")}'
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41
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42 ## Postprocessing
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43 && mv 'out/output.${gxy2omsext("featurexml")}' '$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="csv" argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
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53 <param name="featureXML" argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
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54 <param name="FDR_cutoff" argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
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55 <expand macro="adv_opts_macro">
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56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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57 <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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58 <expand macro="list_string_san"/>
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59 </param>
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60 </expand>
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61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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63 </param>
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64 </inputs>
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65 <outputs>
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66 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <expand macro="autotest_OpenSwathRewriteToFeatureXML"/>
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73 <expand macro="manutest_OpenSwathRewriteToFeatureXML"/>
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74 </tests>
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75 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
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76
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77
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78 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
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79 <expand macro="references"/>
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80 </tool>