Mercurial > repos > chrisd > coverage_sampler
changeset 4:ce65eb39d175 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit cd089c5ccfa100bc4082861964f21c4d612dd49b
| author | chrisd |
|---|---|
| date | Tue, 22 Mar 2016 16:28:39 -0400 |
| parents | 2abae39582d3 |
| children | 17bce2f348b6 |
| files | gene_fraction.xml test-data/ref.fa test-data/result.txt test-data/test.sam |
| diffstat | 2 files changed, 4 insertions(+), 11 deletions(-) [+] |
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--- a/gene_fraction.xml Wed Feb 24 14:27:51 2016 -0500 +++ b/gene_fraction.xml Tue Mar 22 16:28:39 2016 -0400 @@ -25,7 +25,7 @@ <param name="max" type="integer" label="Ending sample level" value="1" min="1" max="100" help="(-max)" /> <param name="threshold" type="integer" label="Gene threshold" - value="1" min="1" max="100" help="(-t)" /> + value="0" min="0" max="100" help="(-t)" /> <param name="skip" type="integer" label="Amount of levels to skip" value="1" min="1" max="100" help="(-skip)" /> <param name="samples" type="integer" label="Amount of samples per level" @@ -42,16 +42,15 @@ </test> </tests> <help><![CDATA[ - This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads. -Program: Coverage Sampler -Contact: Chris Dean <cdean11@rams.colostate.edu +Program: Coverage Sampler + +Contact: Chris Dean <cdean11@rams.colostate.edu> Usage: csa [options] Options: - -amr_fp amr database path -sam_fp sam file path -min starting level @@ -59,10 +58,6 @@ -skip amount of levels to skip -t gene fraction threshold -samples amount of samples per level - -d directory parsing - -bam bam file parsing -out_fp output file path - - ]]></help> </tool>