Mercurial > repos > matt-shirley > ncbi_sra_toolkit
diff sam_dump.xml @ 8:558a88cd49e4
bump toolkit versions, old registration path
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Thu, 13 Mar 2014 16:11:04 -0400 |
| parents | 548b3e8d7a0a |
| children | 393a04ec0fa9 |
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--- a/sam_dump.xml Thu Mar 13 16:08:12 2014 -0400 +++ b/sam_dump.xml Thu Mar 13 16:11:04 2014 -0400 @@ -1,7 +1,7 @@ <tool id="sam_dump" name="Extract reads" version="1.1.2"> <description> in SAM format from NCBI SRA.</description> <command> - sam-dump --log-level fatal + sam-dump --log-level fatal #if str( $region ) != "": --aligned-region $region #end if @@ -14,7 +14,7 @@ #if $header == "yes": --header #else: - --no-header + --no-header #end if #if str( $alignments ) == "both": --unaligned @@ -31,12 +31,12 @@ #if $input.input_select == "file": $input.file #elif $input.input_select == "accession_number": - $input.accession + $input.accession #elif $input.input_select == "text": `cat $input.text` #end if > $output - </command> + </command> <version_string>sam-dump --version</version_string> <inputs> <conditional name="input"> @@ -88,12 +88,12 @@ </data> </outputs> <requirements> - <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> + <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> </requirements> <help> - This tool extracts reads from sra archives using sam-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> -</tool> \ No newline at end of file +</tool>