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comparison extract_files_from_re_archive.xml @ 27:eefed7a82001 draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 12:59:29 +0000
parents 36c418bca8b2
children ba970b24e48c
comparison
equal deleted inserted replaced
26:93595f42a04d 27:eefed7a82001
1 <tool id="extract_var_files_from_re" name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3"> 1 <tool id="extract_var_files_from_re"
2 <command detect_errors="exit_code"> 2 name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3">
3 <command detect_errors="exit_code">
4 <![CDATA[
5
6
3 7
4 #for $sf in $file: 8 #for $sf in $file:
5
6 #if $sf == "CLUSTER_TABLE.csv" 9 #if $sf == "CLUSTER_TABLE.csv"
7 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${cluster_table} 10 mkdir -p tempdir
11 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
12 find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table}
13 rm -r tempdir
8 ; 14 ;
9 #end if 15 #end if
10 16
11 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv" 17 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
12 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${comparative_analysis_count} 18 mkdir -p tempdir
19 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
20 find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count}
21 rm -r tempdir
13 ; 22 ;
14 #end if 23 #end if
15 24
16 #if $sf == "SUPERCLUSTER_TABLE.csv" 25 #if $sf == "SUPERCLUSTER_TABLE.csv"
17 unzip -p -j ${RepeatExplorer_archive} ${sf} &gt; ${supercluster_table} 26 mkdir -p tempdir
18 ; 27 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
28 find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table}
29 rm -r tempdir
19 #end if 30 #end if
20 31
21 #end for 32 #end for
22 33
34 ]]>
23 35
24 36
25 </command> 37 </command>
26
27 <inputs>
28 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
29 38
30 <param name="file" type="select" label="select files you want to extract" multiple="true" optional="false"> 39 <inputs>
40 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results"
41 type="data" format="zip"/>
42
43 <param name="file" type="select" label="select files you want to extract"
44 multiple="true" optional="false">
31 <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option> 45 <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
32 <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">COMPARATIVE_ANALYSIS_COUNTS.csv</option> 46 <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">
47 COMPARATIVE_ANALYSIS_COUNTS.csv
48 </option>
33 <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option> 49 <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
34 </param> 50 </param>
35 </inputs> 51 </inputs>
36 52
37 <outputs> 53 <outputs>
38 <data format="tabular" name="cluster_table" label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}" > 54 <data format="tabular" name="cluster_table"
39 <filter>"CLUSTER_TABLE.csv" in file</filter> 55 label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
40 </data> 56 <filter>"CLUSTER_TABLE.csv" in file</filter>
41 <data format="tabular" name="supercluster_table" label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}"> 57 </data>
42 <filter>"SUPERCLUSTER_TABLE.csv" in file</filter> 58 <data format="tabular" name="supercluster_table"
43 </data> 59 label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
44 <data format="tabular" name="comparative_analysis_count" label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}"> 60 <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
45 <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter> 61 </data>
46 </data> 62 <data format="tabular" name="comparative_analysis_count"
47 </outputs> 63 label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
64 <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
65 </data>
66 </outputs>
48 </tool> 67 </tool>
49 68