Mercurial > repos > galaxyp > openms_qccalculator

annotate QCCalculator.xml @ 8:5f8715a13da8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:15:07 -0400
parents 1fc9e74f040c
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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="QCCalculator" name="QCCalculator" version="2.3.0">
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5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">QCCalculator</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[QCCalculator
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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_out:
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19 -out $param_out
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20 #end if
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21 #if $param_id:
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22 -id $param_id
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23 #end if
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24 #if $param_feature:
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25 -feature $param_feature
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26 #end if
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27 #if $param_consensus:
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28 -consensus $param_consensus
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29 #end if
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30 #if $param_remove_duplicate_features:
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31 -remove_duplicate_features
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32 #end if
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33 #if $adv_opts.adv_opts_selector=='advanced':
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34 #if $adv_opts.param_force:
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35 -force
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36 #end if
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <param name="param_in" type="data" format="mzml" optional="False" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help="(-in) "/>
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41 <param name="param_id" type="data" format="idxml" optional="True" label="Input idXML file containing the identifications" help="(-id) Your identifications will be exported in an easy-to-read format"/>
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42 <param name="param_feature" type="data" format="featurexml" optional="True" label="feature input file (this is relevant for most QC issues)" help="(-feature) "/>
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43 <param name="param_consensus" type="data" format="consensusxml" optional="True" label="consensus input file (this is only used for charge state deconvoluted output" help="(-consensus) Use the consensusXML output form the DeCharger)"/>
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44 <param name="param_remove_duplicate_features" display="radio" type="boolean" truevalue="-remove_duplicate_features" falsevalue="" checked="false" optional="True" label="This flag should be set, if you work with a set of merged features" help="(-remove_duplicate_features) "/>
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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="qcml"/>
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51 </outputs>
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52 <help>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
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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_QCCalculator.html</help>
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56 </tool>