annotate extract_files_from_re_archive.xml @ 33:f1738f8649b0 draft

planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
author petr-novak
date Fri, 04 Aug 2023 08:09:40 +0000
parents cab41d23e2a3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
1 <tool id="extract_var_files_from_re"
30
cab41d23e2a3 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 28
diff changeset
2 name="Extract various files from RepeatExplorer2 archive" version="1.0.0.4">
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
3 <command detect_errors="exit_code">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
4 <![CDATA[
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
5
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
6
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
7
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
8 #for $sf in $file:
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
9 #if $sf == "CLUSTER_TABLE.csv"
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
10 mkdir -p tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
11 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
12 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
13 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
14 find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table}
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
15 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
16 rm -r tempdir
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
17 ;
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
18 #end if
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
19
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
20 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
21 mkdir -p tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
22 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
23 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
24 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
25 find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count}
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
26 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
27 rm -r tempdir
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
28 ;
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
29 #end if
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
30
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
31 #if $sf == "SUPERCLUSTER_TABLE.csv"
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
32 mkdir -p tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
33 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
34 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
35 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
36 find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table}
28
ba970b24e48c planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 27
diff changeset
37 &&
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
38 rm -r tempdir
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
39 #end if
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
40
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
41 #end for
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
42
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
43 ]]>
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
44
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
45
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
46 </command>
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
47
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
48 <inputs>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
49 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results"
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
50 type="data" format="zip"/>
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
51
27
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
52 <param name="file" type="select" label="select files you want to extract"
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
53 multiple="true" optional="false">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
54 <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
55 <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
56 COMPARATIVE_ANALYSIS_COUNTS.csv
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
57 </option>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
58 <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
59 </param>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
60 </inputs>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
61
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
62 <outputs>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
63 <data format="tabular" name="cluster_table"
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
64 label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
65 <filter>"CLUSTER_TABLE.csv" in file</filter>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
66 </data>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
67 <data format="tabular" name="supercluster_table"
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
68 label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
69 <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
70 </data>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
71 <data format="tabular" name="comparative_analysis_count"
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
72 label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
73 <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
74 </data>
eefed7a82001 planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 23
diff changeset
75 </outputs>
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
76 </tool>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
77