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comparison fastq_dump.xml @ 13:c38286ea7047 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 11:44:12 -0400
parents 6c60903f70ac
children f5ea3ce9b9b0
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12:5534eb46de20 13:c38286ea7047
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>fastq-dump --version</version_command> 7 <version_command>fastq-dump --version</version_command>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 9
10 10 @SET_ACCESSIONS@
11 #if $input.input_select=="file_list":
12
13 for acc in `cat $input.file_list` ;
14 do
15
16 #elif $input.input_select=="accession_number":
17
18 ## Stripping leading and trailing spaces in case user typed them in
19 acc="${input.accession}" &&
20
21 #end if
22
23 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
24
25 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
26
27 #end if
28 11
29 ## Need to set the home directory to the current working directory, 12 ## Need to set the home directory to the current working directory,
30 ## 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
31 ## with a cluster manager. 14 ## with a cluster manager.
32 export HOME=\$PWD && 15 export HOME=\$PWD &&