Mercurial > repos > galaxyp > openms_databasefilter

annotate DatabaseFilter.xml @ 9:3fb6d46da3db draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:51:10 -0400
parents 0617defc2f4d
children 21c4273d1890
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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="2.3.0">
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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 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command detect_errors="aggressive"><![CDATA[DatabaseFilter
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_id:
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19 -id $param_id
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20 #end if
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21 #if $param_method:
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22 -method
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23 #if " " in str($param_method):
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24 "$param_method"
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25 #else
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26 $param_method
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27 #end if
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28 #end if
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29 #if $param_out:
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30 -out $param_out
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31 #end if
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32 #if $adv_opts.adv_opts_selector=='advanced':
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33 #if $adv_opts.param_force:
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34 -force
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35 #end if
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <param name="param_in" type="data" format="fasta" optional="False" label="Input FASTA file, containing a database" help="(-in) "/>
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40 <param name="param_id" type="data" format="idxml,mzid" optional="False" label="Input file containing identified peptides and proteins" help="(-id) "/>
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41 <param name="param_method" display="radio" type="select" optional="False" value="whitelist" label="Switch between white-/blacklisting" help="(-method) ">
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42 <option value="whitelist" selected="true">whitelist</option>
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43 <option value="blacklist">blacklist</option>
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44 </param>
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45 <expand macro="advanced_options">
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46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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47 </expand>
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48 </inputs>
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49 <outputs>
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50 <data name="param_out" format="fasta"/>
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51 </outputs>
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52 <help>Filters a protein database (FASTA format) based on identified proteins
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53
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54
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55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DatabaseFilter.html</help>
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56 </tool>