Mercurial > repos > galaxyp > openms_openswathconfidencescoring

annotate OpenSwathConfidenceScoring.xml @ 10:e8f64a7dc470 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:26:13 +0000
parents 401b29d0f88c
children fa73919cc97e
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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="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Compute confidence scores for OpenSwath results</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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($in.ext)' &&
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21 mkdir lib &&
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22 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
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23 mkdir out &&
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24 #if $trafo:
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25 mkdir trafo &&
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26 ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
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27 #end if
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29 ## Main program call
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401b29d0f88c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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37 -lib
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38 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
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39 -out
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40 'out/output.${gxy2omsext("featurexml")}'
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41 #if $trafo:
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42 -trafo
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43 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)'
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44 #end if
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45
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46 ## Postprocessing
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47 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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50 #end if]]></command>
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51 <configfiles>
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52 <inputs name="args_json" data_style="paths"/>
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53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
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57 <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
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58 <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
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59 <param name="decoys" argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
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60 <param name="transitions" argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
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61 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
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62 <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
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63 <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
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64 <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
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65 </section>
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66 <expand macro="adv_opts_macro">
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67 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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68 <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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69 <expand macro="list_string_san"/>
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70 </param>
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71 </expand>
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72 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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74 </param>
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75 </inputs>
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76 <outputs>
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77 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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80 </data>
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81 </outputs>
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82 <tests>
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83 <expand macro="autotest_OpenSwathConfidenceScoring"/>
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84 <expand macro="manutest_OpenSwathConfidenceScoring"/>
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85 </tests>
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86 <help><![CDATA[Compute confidence scores for OpenSwath results
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87
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88
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89 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathConfidenceScoring.html]]></help>
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90 <expand macro="references"/>
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91 </tool>