Mercurial > repos > galaxyp > openms_dtaextractor

annotate DTAExtractor.xml @ 14:856b0f25f4cc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 15:01:29 +0000
parents e31fe5424cbe
children d8b1ec05fbd7
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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="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Extracts spectra of an MS run file to several files in DTA format.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DTAExtractor</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($in.ext)' &&
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22 ## Main program call
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23
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24 set -o pipefail &&
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25 @EXECUTABLE@ -write_ctd ./ &&
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26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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28 -in
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29 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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30 | tee '$stdout'
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32 ## Postprocessing
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
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42 <param name="out" argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
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43 <expand macro="list_string_san"/>
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44 </param>
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45 <param name="mz" argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
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46 <expand macro="list_string_san"/>
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47 </param>
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48 <param name="rt" argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
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49 <expand macro="list_string_san"/>
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50 </param>
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51 <param name="level" argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
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52 <expand macro="list_string_san"/>
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53 </param>
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54 <expand macro="adv_opts_macro">
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55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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56 <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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57 <expand macro="list_string_san"/>
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58 </param>
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59 </expand>
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60 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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66 <filter>OPTIONAL_OUTPUTS is None</filter>
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67 </data>
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68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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70 </data>
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71 </outputs>
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72 <tests>
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73 <expand macro="autotest_DTAExtractor"/>
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74 <expand macro="manutest_DTAExtractor"/>
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75 </tests>
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76 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
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78
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79 For more information, visit http://www.openms.de/documentation/TOPP_DTAExtractor.html]]></help>
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80 <expand macro="references"/>
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8d5dc126d30b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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81 </tool>