annotate DTAExtractor.xml @ 11:fd0630ab8463 draft

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date Wed, 15 May 2019 08:29:31 -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 CTDConverter.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="DTAExtractor" name="DTAExtractor" version="2.3.0">
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5 <description>Extracts spectra of an MS run file to several files in DTA format.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DTAExtractor</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[DTAExtractor
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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 $param_mz:
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22 -mz "$param_mz"
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23 #end if
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24 #if $param_rt:
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25 -rt "$param_rt"
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26 #end if
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27 #if $param_level:
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28 -level "$param_level"
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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 &gt; $param_stdout
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36 ]]></command>
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37 <inputs>
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38 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
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39 <param name="param_out" type="text" size="30" label="base name of DTA output files (RT, m/z and extension are appended)" help="(-out) ">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="'"/>
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43 <remove value="&quot;"/>
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44 </valid>
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45 </sanitizer>
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46 </param>
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47 <param name="param_mz" type="text" size="30" value=":" label="m/z range of precursor peaks to extract" help="(-mz) &lt;br&gt;This option is ignored for MS level 1">
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48 <sanitizer>
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49 <valid initial="string.printable">
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50 <remove value="'"/>
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51 <remove value="&quot;"/>
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52 </valid>
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53 </sanitizer>
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54 </param>
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55 <param name="param_rt" type="text" size="30" value=":" label="retention time range of spectra to extract" help="(-rt) ">
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56 <sanitizer>
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57 <valid initial="string.printable">
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58 <remove value="'"/>
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59 <remove value="&quot;"/>
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 <param name="param_level" type="text" size="30" value="1,2,3" label="MS levels to extract" help="(-level) ">
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64 <sanitizer>
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65 <valid initial="string.printable">
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66 <remove value="'"/>
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67 <remove value="&quot;"/>
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68 </valid>
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69 </sanitizer>
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70 </param>
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71 <expand macro="advanced_options">
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72 <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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73 </expand>
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74 </inputs>
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75 <outputs>
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76 <data name="param_stdout" format="txt" label="Output from stdout"/>
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77 </outputs>
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78 <help>Extracts spectra of an MS run file to several files in DTA format.
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79
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80
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81 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_DTAExtractor.html</help>
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82 </tool>