comparison convert.xml @ 21:c46406466625 draft

Uploaded
author wolma
date Sat, 11 Jun 2016 19:10:44 -0400
parents 93db2f9bca12
children 5db0545b9004
comparison
equal deleted inserted replaced
20:aba6d9b1c1f1 21:c46406466625
2 <description>between different sequence data formats</description> 2 <description>between different sequence data formats</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>mimodd version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz": 9 #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
10 echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups; 10 echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
11 11
12 mkdir converted_data; 12 mkdir converted_data;
13 #end if 13 #end if
14 14
15 mimodd convert 15 python3 -m MiModD convert
16 16
17 #for $i in $mode.input_list 17 #for $i in $mode.input_list
18 "${i.file1}" 18 "${i.file1}"
19 #if $str($mode.iformat) in ("fastq_pe", "gz_pe"): 19 #if $str($mode.iformat) in ("fastq_pe", "gz_pe"):
20 "${i.file2}" 20 "${i.file2}"