Mercurial > repos > iuc > busco
comparison busco.xml @ 1:87983967544b draft
planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
| author | iuc |
|---|---|
| date | Tue, 24 Jan 2017 12:08:38 -0500 |
| parents | 5e3543b1ef9f |
| children | 382a4c19007f |
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| 0:5e3543b1ef9f | 1:87983967544b |
|---|---|
| 13 -o "busco_galaxy" | 13 -o "busco_galaxy" |
| 14 --cpu \${GALAXY_SLOTS:-4} | 14 --cpu \${GALAXY_SLOTS:-4} |
| 15 --evalue ${adv.evalue} | 15 --evalue ${adv.evalue} |
| 16 ${adv.long} | 16 ${adv.long} |
| 17 --limit ${adv.limit} | 17 --limit ${adv.limit} |
| 18 --species ${adv.species} | 18 #if $adv.species: |
| 19 --species '${adv.species}' | |
| 20 #end if | |
| 19 --tarzip | 21 --tarzip |
| 20 ]]></command> | 22 ]]></command> |
| 21 | 23 |
| 22 <inputs> | 24 <inputs> |
| 23 | 25 |
| 37 </param> | 39 </param> |
| 38 | 40 |
| 39 <section name="adv" title="Advanced Options" expanded="False"> | 41 <section name="adv" title="Advanced Options" expanded="False"> |
| 40 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> | 42 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> |
| 41 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> | 43 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> |
| 42 <param argument="--species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> | 44 <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/> |
| 43 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/> | 45 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/> |
| 44 </section> | 46 </section> |
| 45 </inputs> | 47 </inputs> |
| 46 <outputs> | 48 <outputs> |
| 47 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/> | 49 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/> |