Mercurial > repos > iuc > colibread_takeabreak

comparison takeabreak.xml @ 1:a018b8f663ea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author iuc
date Fri, 24 Nov 2017 12:49:52 -0500
parents e1fdaacdabc3
children b0e311ac462c
comparison
equal deleted inserted replaced
0:e1fdaacdabc3 1:a018b8f663ea
11 11
12 ## if single reads 12 ## if single reads
13 #if str( $input_type_option.input_type ) == "simple" 13 #if str( $input_type_option.input_type ) == "simple"
14 #for $input in $input_type_option.reads 14 #for $input in $input_type_option.reads
15 #if $input 15 #if $input
16 #set $filename = str($input)+ "." + $input.ext 16 #set $filename = os.path.basename(str($input)) + "." + $input.ext
17 ln -sf '${input}' '${filename}' && 17 ln -sf '${input}' '${filename}' &&
18 echo "${filename}" >> input.fof && 18 echo "${filename}" >> input.fof &&
19 #end if 19 #end if
20 #end for 20 #end for
21 #else 21 #else
22 ## if paired reads in a list 22 ## if paired reads in a list
23 #for $i, $list in enumerate( $input_type_option.reads_lists ) 23 #for $i, $list in enumerate( $input_type_option.reads_lists )
24 #for $read in $list.list_reads 24 #for $read in $list.list_reads
25 #set $filename = str($read) + "." + $read.ext 25 #set $filename = os.path.basename(str($read)) + "." + $read.ext
26 ln -sf '${read}' '${filename}' && 26 ln -sf '${read}' '${filename}' &&
27 echo "${filename}" >> "indiv_${i}.fof" && 27 echo "${filename}" >> "indiv_${i}.fof" &&
28 #end for 28 #end for
29 echo "indiv_${i}.fof" >> input.fof && 29 echo "indiv_${i}.fof" >> input.fof &&
30 #end for 30 #end for