Mercurial > repos > petr-novak > re_utils
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 |
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 | 7 |
8 #for $sf in $file: | |
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 | 17 ; |
18 #end if | |
19 | |
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 | 28 ; |
29 #end if | |
30 | |
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 | 39 #end if |
40 | |
41 #end for | |
42 | |
27
eefed7a82001
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
23
diff
changeset
|
43 ]]> |
17 | 44 |
45 | |
27
eefed7a82001
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
23
diff
changeset
|
46 </command> |
17 | 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 | 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 | 76 </tool> |
77 |