Mercurial > repos > galaxyp > openms_databasefilter

annotate DatabaseFilter.xml @ 13:56c9ad9cdb65 draft

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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 20:11:58 +0000
parents 0c98acedb17a
children 0878a55de9e7
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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="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Filters a protein database (FASTA format) based on identified proteins</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DatabaseFilter</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($in.ext)' &&
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21 mkdir id &&
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22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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23 mkdir out &&
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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33 -id
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34 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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35 -out
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36 'out/output.${gxy2omsext("fasta")}'
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38 ## Postprocessing
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39 && mv 'out/output.${gxy2omsext("fasta")}' '$out'
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40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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42 #end if]]></command>
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43 <configfiles>
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44 <inputs name="args_json" data_style="paths"/>
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45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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46 </configfiles>
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47 <inputs>
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48 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
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49 <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
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50 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Switch between white-/blacklisting" help="">
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51 <option value="whitelist" selected="true">whitelist</option>
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52 <option value="blacklist">blacklist</option>
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53 <expand macro="list_string_san"/>
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54 </param>
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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="Overrides 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" optional="true" multiple="true" label="Optional outputs">
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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 ${on_string}: out" format="fasta"/>
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67 <data name="ctd_out" format="xml" label="${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_DatabaseFilter"/>
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73 <expand macro="manutest_DatabaseFilter"/>
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74 </tests>
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75 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
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77
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78 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DatabaseFilter.html]]></help>
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79 <expand macro="references"/>
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80 </tool>