Mercurial > repos > galaxyp > openms_ticcalculator

annotate TICCalculator.xml @ 8:60d1971a0cf4 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 09:56:14 -0400
parents 488ea525e0b1
children 32667824b653
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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="TICCalculator" name="TICCalculator" version="2.3.0">
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5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TICCalculator</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[TICCalculator
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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 $param_read_method:
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19 -read_method
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20 #if " " in str($param_read_method):
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21 "$param_read_method"
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22 #else
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23 $param_read_method
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24 #end if
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25 #end if
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26 #if $param_loadData:
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27 -loadData
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28 #if " " in str($param_loadData):
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29 "$param_loadData"
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30 #else
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31 $param_loadData
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32 #end if
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33 #end if
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34 #if $adv_opts.adv_opts_selector=='advanced':
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35 #if $adv_opts.param_force:
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36 -force
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37 #end if
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38 #end if
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39 &gt; $param_stdout
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40 ]]></command>
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41 <inputs>
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42 <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
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43 <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) ">
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44 <option value="regular" selected="true">regular</option>
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45 <option value="indexed">indexed</option>
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46 <option value="indexed_parallel">indexed_parallel</option>
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47 <option value="streaming">streaming</option>
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48 <option value="cached">cached</option>
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49 <option value="cached_parallel">cached_parallel</option>
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50 </param>
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51 <param name="param_loadData" display="radio" type="select" optional="False" value="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help="(-loadData) ">
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52 <option value="true" selected="true">true</option>
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53 <option value="false">false</option>
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54 </param>
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55 <expand macro="advanced_options">
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56 <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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57 </expand>
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58 </inputs>
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59 <outputs>
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60 <data name="param_stdout" format="txt" label="Output from stdout"/>
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61 </outputs>
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62 <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
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63
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64
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65 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TICCalculator.html</help>
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66 </tool>