Mercurial > repos > iuc > sra_tools
diff fastq_dump.xml @ 2:f256cb398262 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author | iuc |
---|---|
date | Fri, 16 Sep 2016 17:24:03 -0400 |
parents | 462ee06c9358 |
children | 4732693f4661 |
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--- a/fastq_dump.xml Tue May 17 14:14:50 2016 -0400 +++ b/fastq_dump.xml Fri Sep 16 17:24:03 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_dump" name="Extract reads" version="1.3.0"> +<tool id="fastq_dump" name="Extract reads" version="2.6.2"> <description>in FASTQ/A format from NCBI SRA.</description> <macros> <import>sra_macros.xml</import> @@ -21,10 +21,10 @@ #if $input.input_select=="file_list" or $input.input_select=="accession_number": [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( #end if - + ## Need to set the home directory to the current working directory, - ## else the tool tries to write to home/.ncbi and fails when used - ## with a cluster manager. + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. export HOME=\$PWD && vdb-config --restore-defaults && #if $input.input_select == "file": @@ -76,7 +76,7 @@ #end if $adv.clip $adv.skip_technical - + #if str( $outputformat ) == "fasta": --fasta #end if @@ -97,15 +97,15 @@ #if str( $outputformat ) == "fasta": - + for f in *_2.fasta ; do mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ; mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta" ; done && for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done - + #else: for f in *_2.fastq ; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ; mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq" ; done && for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done - + #end if @@ -114,7 +114,7 @@ #end if - + ]]> </command> <inputs> @@ -202,7 +202,7 @@ This tool extracts reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - + NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively @SRATOOLS_ATTRRIBUTION@ </help>