Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 73:61b7ab692529

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 14:20:36 -0400
parents 306431b9bf86
children 270e8f69228b
comparison
equal deleted inserted replaced
72:306431b9bf86 73:61b7ab692529
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input || exit 1; 9 mkdir -p cpipes-input || exit 1;
10 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
11 #import os
12 #if (str($input_read_type_cond.input_read_type) == "single_long"): 11 #if (str($input_read_type_cond.input_read_type) == "single_long"):
13 #for $key in $input_read_type_cond.input.keys() 12 #for $key in $input_read_type_cond.input.keys()
14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; 13 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
15 #end for 14 #end for
16 #elif (str($input_read_type_cond.input_read_type) == "paired"): 15 #elif (str($input_read_type_cond.input_read_type) == "paired"):
17 #for _, $pair in enumerate($input_read_type_cond.input_pair) 16 #for _, $pair in enumerate($input_read_type_cond.input_pair)
18 #set $read_R1 = os.path.basename(str($pair.forward)) 17 #set read_R1_name = str($pair.forward.name)
19 #set $read_R2 = os.path.basename(str($pair.reverse)) 18 #set read_R2_name = str($pair.reverse.name)
20 #set $read_R1_name = str($read_R1.name)
21 #set $read_R2_name = str($read_R2.name)
22 ln -sf '$pair.forward' './cpipes-input/$read_R1_name'; 19 ln -sf '$pair.forward' './cpipes-input/$read_R1_name';
23 ln -sf '$pair.reverse' './cpipes-input/$read_R2_name'; 20 ln -sf '$pair.reverse' './cpipes-input/$read_R2_name';
24 #end for 21 #end for
25 #end if 22 #end if
26 $__tool_directory__/0.2.1/cpipes 23 $__tool_directory__/0.2.1/cpipes