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comparison fastq_dump.xml @ 5:6f68b86da01a draft default tip

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
author mvdbeek
date Wed, 30 Sep 2015 11:47:04 -0400
parents 68527898a9ea
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4:b9408bf2a9ac 5:6f68b86da01a
1 <tool id="fastq_dump" name="Extract reads" version="1.2.4"> 1 <tool id="fastq_dump" name="Extract reads" version="1.2.5">
2 <description>in FASTQ/A format from NCBI SRA.</description> 2 <description>in FASTQ/A format from NCBI SRA.</description>
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 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 ## Need to set the home directory to the current working directory, 9 ## Need to set the home directory to the current working directory,
10 ## else the tool tries to write to home/.ncbi and fails when used 10 ## else the tool tries to write to home/.ncbi and fails when used
11 ## with a cluster manager. 11 ## within production environments.
12 export HOME=\$PWD; 12 export HOME=\$PWD;
13 vdb-config --restore-defaults; 13 vdb-config --restore-defaults;
14 #if $input.input_select == "file": 14 #if $input.input_select == "file":
15 fastq-dump --log-level fatal --accession '${input.file.name}' 15 fastq-dump --log-level fatal --accession '${input.file.name}'
16 #else: 16 #else: