Mercurial > repos > matt-shirley > sra_tools
changeset 38:a0925f507352 draft
bring pileup to parity with sam; fixed minMapq for sam
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Sun, 04 Aug 2013 23:17:53 -0400 |
| parents | 4da2d7f0128e |
| children | 1d152e8cb375 |
| files | sam_dump.xml sra_pileup.xml |
| diffstat | 2 files changed, 33 insertions(+), 6 deletions(-) [+] |
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--- a/sam_dump.xml Thu Aug 01 13:57:27 2013 -0400 +++ b/sam_dump.xml Sun Aug 04 23:17:53 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="sam_dump" name="Extract reads" version="1.1.0"> +<tool id="sam_dump" name="Extract reads" version="1.1.1"> <description> in SAM format from NCBI SRA.</description> <command> sam-dump --log-level fatal @@ -8,6 +8,9 @@ #if str( $matepairDist ) != "": --matepair-distance $matepairDist #end if + #if str( $minMapq ) != "": + --minmapq $minMapq + #end if #if $header == "yes": --header #else:
--- a/sra_pileup.xml Thu Aug 01 13:57:27 2013 -0400 +++ b/sra_pileup.xml Sun Aug 04 23:17:53 2013 -0400 @@ -1,18 +1,42 @@ -<tool id="sra_pileup" name="Generate pileup format" version="1.0.0"> +<tool id="sra_pileup" name="Generate pileup format" version="1.0.1"> <description> from NCBI sra.</description> - <command>sra-pileup '$input' > $output</command> + <command>sra-pileup --log-level fatal + #if str( $region ) != "": + --aligned-region $region + #end if + #if str( $minMapq ) != "": + --minmapq $minMapq + #end if + #if $input.input_select == "file": + $input.file + #else: + $input.accession + #end if + > $output</command> <version_string>sra-pileup --version</version_string> <inputs> - <param format="sra" name="input" type="data" label="sra archive"/> + <conditional name="input"> + <param name="input_select" type="select" label="select input type"> + <option value="accession_number">SRR accession</option> + <option value="file">SRA archive in current history</option> + </param> + <when value="file"> + <param format="sra" name="file" type="data" label="sra archive"/> + </when> + <when value="accession_number"> + <param format="text" name="accession" type="text" label="accession"/> + </when> + </conditional> + <param format="text" name="region" type="text" label="aligned region"/> + <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> </inputs> <outputs> - <data format="sam" name="output"/> + <data format="pileup" name="output"/> </outputs> <requirements> <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> - !!! Note that this tool does not function correctly !!! This tool produces pileup format from sra archives using sra-pileup. The sra-pileup 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.