Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/ParseBlastForUniqueMatch.xml @ 7:3f7b0788a1c4 draft
Uploaded
| author | mcharles |
|---|---|
| date | Tue, 07 Oct 2014 10:34:34 -0400 |
| parents | 442a7c88b886 |
| children | 0a6c1cfe4dc8 |
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| 6:1776b8ddd87e | 7:3f7b0788a1c4 |
|---|---|
| 1 <tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01"> | 1 <tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01"> |
| 2 <description>Filter mpileup with blast results</description> | 2 <description>Filter mpileup with blast results</description> |
| 3 <command interpreter="perl"> | 3 <command interpreter="perl"> |
| 4 ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file | 4 ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file |
| 5 </command> | 5 </command> |
| 6 <inputs> | 6 <inputs> |
| 7 <param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> | 7 <param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> |
| 8 <param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/> | 8 <param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/> |
| 9 <param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> | 9 <param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> |
| 10 <param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/> | 10 <param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/> |
| 11 </inputs> | 11 </inputs> |
| 12 <outputs> | 12 <outputs> |
| 13 <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/> | 13 <data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/> |
| 14 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> | |
| 14 </outputs> | 15 </outputs> |
| 15 | 16 |
| 16 <help> | 17 <help> |
| 17 | 18 |
| 18 | 19 |