Mercurial > repos > petr-novak > re_utils

annotate extract_files_from_re_archive.xml @ 27:eefed7a82001 draft

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author petr-novak
date Wed, 02 Aug 2023 12:59:29 +0000
parents 36c418bca8b2
children ba970b24e48c
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1 <tool id="extract_var_files_from_re"
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2 name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3">
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3 <command detect_errors="exit_code">
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4 <![CDATA[
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8 #for $sf in $file:
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9 #if $sf == "CLUSTER_TABLE.csv"
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10 mkdir -p tempdir
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11 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
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12 find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table}
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13 rm -r tempdir
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14 ;
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15 #end if
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17 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
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18 mkdir -p tempdir
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19 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
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20 find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count}
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21 rm -r tempdir
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22 ;
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23 #end if
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25 #if $sf == "SUPERCLUSTER_TABLE.csv"
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26 mkdir -p tempdir
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27 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
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28 find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table}
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29 rm -r tempdir
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30 #end if
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32 #end for
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34 ]]>
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37 </command>
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39 <inputs>
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40 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results"
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41 type="data" format="zip"/>
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43 <param name="file" type="select" label="select files you want to extract"
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44 multiple="true" optional="false">
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45 <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
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46 <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">
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47 COMPARATIVE_ANALYSIS_COUNTS.csv
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48 </option>
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49 <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
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50 </param>
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51 </inputs>
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53 <outputs>
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54 <data format="tabular" name="cluster_table"
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55 label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
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56 <filter>"CLUSTER_TABLE.csv" in file</filter>
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57 </data>
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58 <data format="tabular" name="supercluster_table"
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59 label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
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60 <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
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61 </data>
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62 <data format="tabular" name="comparative_analysis_count"
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63 label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
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64 <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
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65 </data>
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66 </outputs>
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67 </tool>
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