Mercurial > repos > tomnl > dma_filelist_generation

annotate dma-filelist-generation.xml @ 2:21d2cd76bb1b draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
author tomnl
date Thu, 03 May 2018 05:22:17 -0400
parents 6a2bb42acfe4
children
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1 <tool id="dma_filelist_generation" name="dma_filelist_generation" version="0.1.0">
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2 <description>Generate filelist for DMA DIMS nearline</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command interpreter="python"><![CDATA[
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7 dma-filelist-generation.py
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8 -i
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9 #for $i in $library
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10 $__app__.config.user_library_import_dir/$__user_email__/$i.library
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11 #end for
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12 -o .
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13 #if $check_mzml
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14 --check_mzml
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15 #end if
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16 #if $check_raw
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17 --check_raw
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18 #end if
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19 #if $create_filelist_mzml
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20 --create_filelist_mzml
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21 #end if
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22 #if $create_filelist_raw
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23 --create_filelist_raw
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24 #end if
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25
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26 ]]></command>
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28 <inputs>
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30 <repeat name="library" title="Library directories containing *.mzml or *.raw files"
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31 help="multiple directories can be used to make one filelist, for cases where
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32 the files for different classes are in different directories">
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33 <param name="library" type="text" size="40" >
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34 <validator type="empty_field" />
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35 </param>
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36 </repeat>
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37
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38 <param name="check_mzml" checked="true" type="boolean" label="Check mzML files?" help=""/>
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39 <param name="check_raw" checked="true" type="boolean" label="Check raw files?" help=""/>
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40 <param name="create_filelist_mzml" type="boolean" label="Create filelist for mzML files?" help=""/>
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41 <param name="create_filelist_raw" checked="true" type="boolean" label="Create filelist for raw files?" help=""/>
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42
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43
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44 </inputs>
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45 <outputs>
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46 <data name="filelist_mzml" label="${tool.name} on ${on_string}: filelist mzML"
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47 from_work_dir="filelist_mzml.tsv" format="tsv">
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48 <filter>create_filelist_mzml is True</filter>
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49 </data>
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50 <data name="filelist_raw" label="${tool.name} on ${on_string}: filelist raw"
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51 from_work_dir="filelist_raw.tsv" format="tsv">
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52 <filter>create_filelist_raw is True</filter>
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53 </data>
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54
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55 </outputs>
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56 <tests>
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57
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58 </tests>
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59 <help><![CDATA[
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61
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62 ]]></help>
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63 </tool>