Mercurial > repos > bgruening > diamond
changeset 2:09a565cfc192 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 07 Feb 2015 12:19:45 -0500 |
| parents | fbe4eedec466 |
| children | e6ce730fbba6 |
| files | diamand.xml diamand_makedb.xml test-data/diamond_makedb_result1.dmnd |
| diffstat | 3 files changed, 19 insertions(+), 16 deletions(-) [+] |
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--- a/diamand.xml Sat Feb 07 05:32:30 2015 -0500 +++ b/diamand.xml Sat Feb 07 12:19:45 2015 -0500 @@ -47,20 +47,6 @@ ]]> </command> <inputs> - <conditional name="method"> - <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> - <option value="blastp">Align amino acid query sequences (blastp)</option> - <option value="blastx">Align DNA query sequences (blastx)</option> - </param> - <when value="blastp"> - <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> - <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> - </when> - <when value="blastx"> - <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> - <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> - </when> - </conditional> <param name="query" type="data" format="fasta" label="Input query file in FASTA format" /> @@ -85,6 +71,21 @@ </when> <!-- history --> </conditional> + <conditional name="method"> + <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> + <option value="blastp">Align amino acid query sequences (blastp)</option> + <option value="blastx">Align DNA query sequences (blastx)</option> + </param> + <when value="blastp"> + <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> + <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> + </when> + <when value="blastx"> + <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> + <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> + </when> + </conditional> + <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)"> <option value="BLOSUM45">BLOSUM45</option> <option value="BLOSUM50">BLOSUM50</option>
--- a/diamand_makedb.xml Sat Feb 07 05:32:30 2015 -0500 +++ b/diamand_makedb.xml Sat Feb 07 12:19:45 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="bg_diamond_makedb" name="Diamond" version="0.6.13"> +<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13"> <description>Build database from a FASTA file</description> <requirements> <requirement type="package" version="0.6.13">diamond</requirement> @@ -9,7 +9,9 @@ diamond makedb --threads "\${GALAXY_SLOTS:-12}" --in $infile - --db $outfile + --db ./database.dnmd + && + mv ./database.dnmd $outfile ]]> </command> <inputs>