Mercurial > repos > drosofff > msp_cap3
changeset 5:dd02d02ca305 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
| author | drosofff |
|---|---|
| date | Wed, 28 Oct 2015 13:11:29 -0400 |
| parents | 4cf7201615f5 |
| children | e29f3d1124e4 |
| files | cap3.xml |
| diffstat | 1 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/cap3.xml Sat Jun 20 06:16:58 2015 -0400 +++ b/cap3.xml Wed Oct 28 13:11:29 2015 -0400 @@ -1,10 +1,10 @@ -<tool id="cap3" name="cap3" version="1.1.0"> +<tool id="cap3" name="cap3" version="1.2.0"> <description>Sequence Assembly tool</description> <requirements> <requirement type="package" version="3">cap3</requirement> </requirements> <command> -cap3 "$inputSequences" > "$cap3stdout"; +cap3 -o $overlaplength -p overlapidentity "$inputSequences" > "$cap3stdout"; mv "$inputSequences".cap.contigs $contigs; mv "$inputSequences".cap.contigs.qual $contigsqual; mv "$inputSequences".cap.contigs.links $contigslink; @@ -17,6 +17,8 @@ <inputs> <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" /> + <param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" /> + <param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90" help="-p option. must be > 65. 90 by default" /> </inputs> <outputs> @@ -33,6 +35,8 @@ <tests> <test> <param name="inputSequences" value="input.fa" ftype="fasta"/> + <param name="overlaplength" value="40" /> + <param name="overlapidentity" value="90" /> <output name="contigsandsinglets" file="contigsandsinglets.fa"/> <output name="cap3stdout" file="cap3stdout.txt"/> <output name="contigs" file="contigs.fa"/>