Mercurial > repos > galaxyp > openms_qcimporter

annotate QCImporter.xml @ 13:d29c4c46e057 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:23:03 +0000
parents 0cfaedd90c2b
children 988ae4cfb522
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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: [Utilities]-->
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4 <tool id="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Imports tables with quality control parameters into qcml files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">QCImporter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 #if $in:
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18 mkdir in &&
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19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 #end if
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21 mkdir table &&
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22 ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
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23 mkdir mapping &&
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24 ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
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25 mkdir out &&
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__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 #if $in:
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34 -in
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35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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36 #end if
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37 -table
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38 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)'
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39 -mapping
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40 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)'
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41 -out
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42 'out/output.${gxy2omsext("qcml")}'
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43
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44 ## Postprocessing
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45 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
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46 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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47 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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48 #end if]]></command>
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49 <configfiles>
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50 <inputs name="args_json" data_style="paths"/>
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51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
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55 <param argument="-table" type="data" format="csv" optional="false" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/>
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56 <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without &quot;!) select csv data sets(s)"/>
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57 <expand macro="adv_opts_macro">
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58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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59 <param 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" name="test"/>
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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 ${on_string}: out" format="qcml"/>
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69 <data name="ctd_out" format="xml" label="${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><!--TODO-->
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74 </tests>
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75 <help><![CDATA[Imports tables with quality control parameters into qcml files.
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77
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78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCImporter.html]]></help>
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79 <expand macro="references"/>
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80 </tool>