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Commit message:
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df |
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modified:
blat.xml |
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| diff -r 3511cb739854 -r 9aad7a2258e5 blat.xml --- a/blat.xml Fri Feb 03 13:11:55 2017 -0500 +++ b/blat.xml Wed Apr 12 12:24:53 2017 -0400 |
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| @@ -6,7 +6,7 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ blat - #if $noHead + #if $noHead == "yes" -noHead #end if -q=$query_type @@ -20,23 +20,26 @@ <inputs> <param type="data" name="database" format="fasta" /> <param type="data" name="query" format="fasta" /> - <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dna"> - <option value="dna">DNA sequence</option> - <option value="prot">protein sequence</option> - <option value="dnax">DNA sequence translated in six frames to protein</option> + <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> + <option value="dna">dna - DNA sequence</option> + <option value="prot">prot - protein sequence</option> + <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> </param> - <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is dna"> - <option value="dna">DNA sequence</option> - <option value="rna">RNA sequence</option> - <option value="prot">protein sequence</option> - <option value="dnax">DNA sequence translated in six frames to protein</option> - <option value="rnax">DNA sequence translated in three frames to protein</option> + <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q"> + <option value="dna">dna - DNA sequence </option> + <option value="rna">rna - RNA sequence</option> + <option value="prot">prot - protein sequence</option> + <option value="dnax">dnax - DNA sequence translated in six frames to protein</option> + <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option> </param> - <param name="noHead" type="boolean" value="false" label="Suppresses .psl header (so it's just a tab-separated file)." /> + <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." > + <option value="yes" selected="true">Yes, suppresses .psl header</option> + <option value="no">No, do not suppresses .psl header</option> + </param> <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas - are ignored entirely in protein or translated searches."> - <option value="lower">lower - mask out lower-cased sequence</option> + are ignored entirely in protein or translated searches. Default is lower" argument="-mask"> + <option value="lower" selected="true">lower - mask out lower-cased sequence</option> <option value="upper">upper - mask out upper-cased sequence</option> <option value="out">out - mask according to database.out RepeatMasker .out file</option> <option value="file.out">file.out - mask database according to RepeatMasker file.out</option> |