Mercurial > repos > petr-novak > re_utils

comparison extract_files_from_re_archive.xml @ 28:ba970b24e48c draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 13:09:47 +0000
parents eefed7a82001
children cab41d23e2a3
comparison
equal deleted inserted replaced
27:eefed7a82001 28:ba970b24e48c
6 6
7 7
8 #for $sf in $file: 8 #for $sf in $file:
9 #if $sf == "CLUSTER_TABLE.csv" 9 #if $sf == "CLUSTER_TABLE.csv"
10 mkdir -p tempdir 10 mkdir -p tempdir
11 &&
11 unzip ${RepeatExplorer_archive} ${sf} -d tempdir 12 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
13 &&
12 find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table} 14 find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table}
15 &&
13 rm -r tempdir 16 rm -r tempdir
14 ; 17 ;
15 #end if 18 #end if
16 19
17 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv" 20 #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
18 mkdir -p tempdir 21 mkdir -p tempdir
22 &&
19 unzip ${RepeatExplorer_archive} ${sf} -d tempdir 23 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
24 &&
20 find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count} 25 find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count}
26 &&
21 rm -r tempdir 27 rm -r tempdir
22 ; 28 ;
23 #end if 29 #end if
24 30
25 #if $sf == "SUPERCLUSTER_TABLE.csv" 31 #if $sf == "SUPERCLUSTER_TABLE.csv"
26 mkdir -p tempdir 32 mkdir -p tempdir
33 &&
27 unzip ${RepeatExplorer_archive} ${sf} -d tempdir 34 unzip ${RepeatExplorer_archive} ${sf} -d tempdir
35 &&
28 find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table} 36 find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table}
37 &&
29 rm -r tempdir 38 rm -r tempdir
30 #end if 39 #end if
31 40
32 #end for 41 #end for
33 42