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comparison sam_dump.xml @ 13:74dd3d0a33d1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
author iuc
date Wed, 17 Oct 2018 11:42:38 -0400
parents 73f1fbdea468
children 5c5d6624f8de
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12:34ca8f964219 13:74dd3d0a33d1
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>sam-dump --version</version_command> 7 <version_command>sam-dump --version</version_command>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #if $input.input_select=="file_list": 10 @SET_ACCESSIONS@
11 for acc in `cat $input.file_list` ;
12 do
13 #elif $input.input_select=="accession_number":
14 acc="${input.accession}" &&
15 #end if
16
17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
19 #end if
20 11
21 ## Need to set the home directory to the current working directory, 12 ## Need to set the home directory to the current working directory,
22 ## else the tool tries to write to home/.ncbi and fails when used 13 ## else the tool tries to write to home/.ncbi and fails when used
23 ## with a cluster manager. 14 ## with a cluster manager.
24 export HOME=\$PWD && 15 export HOME=\$PWD &&