Mercurial > repos > iuc > spaln
comparison spaln.xml @ 2:dd0cd2319ae5 draft
"planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
| author | iuc |
|---|---|
| date | Fri, 19 Nov 2021 10:09:15 +0000 |
| parents | 37b5e1f0b544 |
| children | 32c11a4b5dbf |
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| 1:37b5e1f0b544 | 2:dd0cd2319ae5 |
|---|---|
| 36 -yL'${adv.min_intron_len}' | 36 -yL'${adv.min_intron_len}' |
| 37 -yZ'${adv.intron_potential_weight}' | 37 -yZ'${adv.intron_potential_weight}' |
| 38 #if str($adv.max_gene_length).strip() != '' | 38 #if str($adv.max_gene_length).strip() != '' |
| 39 -XG'${adv.max_gene_length}' | 39 -XG'${adv.max_gene_length}' |
| 40 #end if | 40 #end if |
| 41 $adv.format_remote_queries | |
| 42 $adv.salvage_mode | |
| 41 #end if | 43 #end if |
| 42 '$genome' '$query' >'$output1' | 44 '$genome' '$query' >'$output1' |
| 43 ]]></command> | 45 ]]></command> |
| 44 <inputs> | 46 <inputs> |
| 45 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" /> | 47 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" /> |
| 88 <param argument="-yz" name="coding_potential_weight" type="integer" value="2" label="Weight for coding potential" /> | 90 <param argument="-yz" name="coding_potential_weight" type="integer" value="2" label="Weight for coding potential" /> |
| 89 <param argument="-yB" name="branch_point_weight" type="integer" value="0" label="Weight for branch point signal" /> | 91 <param argument="-yB" name="branch_point_weight" type="integer" value="0" label="Weight for branch point signal" /> |
| 90 <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" /> | 92 <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" /> |
| 91 <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" /> | 93 <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" /> |
| 92 <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" /> | 94 <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" /> |
| 95 <param argument="-yX" name="format_remote_queries" type="boolean" checked="false" truevalue="-yX" falsevalue="" label="Format for remote queries" help="More sensitive but less economic than the default" /> | |
| 96 <param argument="-XS" name="salvage_mode" type="boolean" checked="false" truevalue="-XS" falsevalue="" label="Activate salvage mode" help="Examine all positively scored blocks. Considerably slow." /> | |
| 93 </when> | 97 </when> |
| 94 </conditional> | 98 </conditional> |
| 95 </inputs> | 99 </inputs> |
| 96 <outputs> | 100 <outputs> |
| 97 <data name="output1" format="tabular"> | 101 <data name="output1" format="tabular"> |