Mercurial > repos > nilesh > rseqc
diff bam_stat.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children |
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--- a/bam_stat.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/bam_stat.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,26 +1,26 @@ -<tool id="bam_stat" name="BAM/SAM Mapping Stats" version="1.1"> - <description> - reads mapping statistics for a provided BAM or SAM file. - </description> - <requirements> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements>s - <command> - bam_stat.py -i $input -q $mapqual 2> $output - </command> - <inputs> - <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> - <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" /> - </inputs> - <outputs> - <data format="txt" name="output" /> - </outputs> +<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="1.1"> + <description> + reads mapping statistics for a provided BAM or SAM file. + </description> + <requirements> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements>s + <command> + bam_stat.py -i $input -q $mapqual 2> $output + </command> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <inputs> + <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> + <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" /> + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + <help> bam_stat.py +++++++++++ @@ -61,5 +61,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores - </help> + </help> </tool>