Mercurial > repos > galaxyp > openms_speclibcreator

annotate SpecLibCreator.xml @ 7:b854c87823d3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 26556c08813e892b4d1eed0e98012601870cae5f
author galaxyp
date Wed, 20 Sep 2017 10:30:18 -0400
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="SpecLibCreator" name="SpecLibCreator" version="2.2.0">
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5 <description>Creates an MSP formatted spectral library.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpecLibCreator</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>SpecLibCreator
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15 #if $param_info:
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16 -info $param_info
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17 #end if
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18 #if $param_itemseperator:
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19 -itemseperator "$param_itemseperator"
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20 #end if
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21 #if $param_itemenclosed:
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22 -itemenclosed
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23 #end if
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24 #if $param_spec:
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25 -spec $param_spec
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26 #end if
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27 #if $param_out:
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28 -out $param_out
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29 #end if
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_force:
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32 -force
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33 #end if
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/>
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38 <param name="param_itemseperator" type="text" size="30" value="," label=" Separator between items. e.g. ," help="(-itemseperator) ">
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39 <sanitizer>
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40 <valid initial="string.printable">
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41 <remove value="'"/>
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42 <remove value="&quot;"/>
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43 </valid>
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44 </sanitizer>
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45 </param>
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46 <param name="param_itemenclosed" display="radio" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/>
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47 <param name="param_spec" type="data" format="mzData,mzxml" optional="False" label="spectra" help="(-spec) "/>
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48 <expand macro="advanced_options">
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49 <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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50 </expand>
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51 </inputs>
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52 <outputs>
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53 <data name="param_out" format="msp"/>
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54 </outputs>
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55 <help>Creates an MSP formatted spectral library.
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56
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57
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58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html</help>
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59 </tool>