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"planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"
author prog
date Wed, 08 Jan 2020 12:47:49 +0000
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1 <!-- vi: se fdm=marker : -->
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2 <tool id="isa2mzxml" name="ISA to mzXML" version="1.3.0">
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3
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4 <description>Extract mzXML files from an ISA dataset and output a collection of mzXML dataset.</description>
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5
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6 <!-- Command {{{1 -->
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7
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8 <command><![CDATA[
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9 ## @@@BEGIN_CHEETAH@@@
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10
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11 $__tool_directory__/extract-from-isa
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12 -i "$isa.extra_files_path"
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13 -e mzXML
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14 -o mzXML
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15
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16 ## @@@END_CHEETAH@@@
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17 ]]></command>
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18
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19 <!-- Inputs {{{1 -->
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20
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21 <inputs>
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22 <param name="isa" label="ISA" type="data" format="isa-tab"/>
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23 </inputs>
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24
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25 <!-- Outputs {{{1 -->
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26
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27 <outputs>
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28 <collection name="mzXML" type="list" label="mzXML files">
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29 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.[mM][zZ][xX][mM][lL]$" directory="mzXML" format="mzxml"/>
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30 </collection>
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31 </outputs>
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32
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33 <!-- Tests {{{1 -->
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34 <tests>
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35 <test>
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36 <param name="isa" value="mzxml_study.zip" ftype="isa-tab"/>
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37 <output_collection name="mzXML" type="list" count="1">
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38 <element name="empty" file="mzxml_study_output/empty.mzXML" ftype="mzxml"/>
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39 </output_collection>
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40 </test>
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41 </tests>
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42
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43 <!-- Help {{{1 -->
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44 <help>
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45 <!-- @@@BEGIN_RST@@@ -->
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46
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47 ====================
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48 ISA to mzXML
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49 ====================
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50
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51 Extract mzXML files contained inside an ISA archive.
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52
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53 -----
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54 Input
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55 -----
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56
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57 ISA dataset
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58 ===========
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59
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60 The ISA-Tab dataset from which to extract the files.
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61
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62 ------
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63 Output
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64 ------
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65
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66 The output is a collection of mzXML files.
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67
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68 <!-- @@@END_RST@@@ -->
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69 </help>
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70
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71 <!-- Citations {{{1 -->
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72 <citations>
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73 <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
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74 <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
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75 </citations>
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76
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77 </tool>