Mercurial > repos > edward-kirton > hmmer
comparison hmmer.xml @ 2:376092ae10ed draft
reformat output to tabular
| author | Edward Kirton <eskirton@lbl.gov> |
|---|---|
| date | Thu, 30 Aug 2012 11:58:27 -0700 |
| parents | c16d8db9338a |
| children |
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| 1:66f8262e1686 | 2:376092ae10ed |
|---|---|
| 1 <tool id="hmmer" name="hmmer" version="1.0.0"> | 1 <tool id="hmmer" name="hmmer" version="1.0.0"> |
| 2 <description>hmmscan/search seqs vs profiles</description> | 2 <description>hmmscan/search seqs vs profiles</description> |
| 3 <command> | 3 <requirements> |
| 4 <requirement type="package">hmmer</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="perl"> | |
| 7 hmmer_wrapper.pl | |
| 4 $program | 8 $program |
| 5 ##--cpu 8 | 9 --cpu 8 |
| 6 --tblout $tblout | 10 --tblout $tblout |
| 7 --domtblout $domtblout | 11 --domtblout $domtblout |
| 8 $acc | 12 $acc |
| 9 $noali | 13 $noali |
| 10 --notextw | 14 --notextw |
| 124 <outputs> | 128 <outputs> |
| 125 <data name="logfile" format="txt" /> | 129 <data name="logfile" format="txt" /> |
| 126 <data name="tblout" format="tabular" label="${tool.name} on $on_string: Per-sequence hits" /> | 130 <data name="tblout" format="tabular" label="${tool.name} on $on_string: Per-sequence hits" /> |
| 127 <data name="domtblout" format="tabular" label="${tool.name} on $on_string: Per-domain hits" /> | 131 <data name="domtblout" format="tabular" label="${tool.name} on $on_string: Per-domain hits" /> |
| 128 </outputs> | 132 </outputs> |
| 129 <requirements> | |
| 130 <requirement type="binary">hmmscan</requirement> | |
| 131 <requirement type="binary">hmmsearch</requirement> | |
| 132 </requirements> | |
| 133 <tests> | 133 <tests> |
| 134 </tests> | 134 </tests> |
| 135 <help> | 135 <help> |
| 136 .. class:: warningmark | 136 .. class:: warningmark |
| 137 | 137 |