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comparison busco.xml @ 1:0b9b7d845c2a draft

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planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
author iuc
date Tue, 24 Jan 2017 12:08:26 -0500
parents edb07a3e524e
children d010a90f588e
comparison
equal deleted inserted replaced
0:edb07a3e524e 1:0b9b7d845c2a
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"/>