annotate extract_files_from_re_archive.xml @ 17:d14b68e9fd1d draft

Uploaded - new tools added
author petr-novak
date Wed, 28 Apr 2021 08:37:20 +0000
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children 36c418bca8b2
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1 <tool id="extract_var_files_from_re" name="Extract various files from RepeatExplorer2 archive">
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2 <command detect_errors="exit_code">
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3
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4 #for $sf in $file:
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5
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6 #if $sf == "CLUSTER_TABLE.csv"
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7 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${cluster_table}
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8 ;
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9 #end if
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10
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11 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
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12 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${comparative_analysis_count}
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13 ;
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14 #end if
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15
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16 #if $sf == "SUPERCLUSTER_TABLE.csv"
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17 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${supercluster_table}
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18 ;
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19 #end if
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20
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21 #end for
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24
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25 </command>
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27 <inputs>
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28 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
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29
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30 <param name="file" type="select" label="select files you want to extract" multiple="true" optional="false">
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31 <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
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32 <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">COMPARATIVE_ANALYSIS_COUNTS.csv</option>
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33 <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
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34 </param>
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35 </inputs>
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36
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37 <outputs>
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38 <data format="tabular" name="cluster_table" label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}" >
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39 <filter>"CLUSTER_TABLE.csv" in file</filter>
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40 </data>
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41 <data format="tabular" name="supercluster_table" label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
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42 <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
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43 </data>
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44 <data format="tabular" name="comparative_analysis_count" label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
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45 <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
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46 </data>
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47 </outputs>
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48 </tool>
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