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comparison prokka.xml @ 3:5c289bf13a08 draft

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Uploaded
author lionelguy
date Thu, 05 Sep 2013 03:59:23 -0400
parents 2bb7c28ea68f
children 39bc9c61c55b
comparison
equal deleted inserted replaced
2:bb07951d72db 3:5c289bf13a08
73 <option value="neg">negative</option> 73 <option value="neg">negative</option>
74 </param> 74 </param>
75 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" /> 75 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
76 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" /> 76 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
77 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" /> 77 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
78 <param name="cpus" type="integer" value="0" min="0" label="Number of CPUs to use [0=all] " /> 78 <param name="cpus" type="integer" value="4" min="1" label="Number of CPUs to use " />
79 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" /> 79 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
80 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" /> 80 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
81 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" /> 81 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
82 <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" /> 82 <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
83 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" /> 83 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
93 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/> 93 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
94 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/> 94 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/> 95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
96 </outputs> 96 </outputs>
97 <stdio> 97 <stdio>
98 <!--<exit_code range="1:" level="fatal" description="Error" />--> 98 <exit_code range="1:" level="fatal" description="Error" />
99 <regex match="not a readable non-empty FASTA file" 99 <regex match="not a readable non-empty FASTA file"
100 source="stdout" 100 source="both"
101 level="fatal" 101 level="fatal"
102 description="Input file not a readable non-empty FASTA file" /> 102 description="Input file not a readable non-empty FASTA file" />
103 <regex match="Illegal division by zero"
104 source="both"
105 level="fatal"
106 description="Illegal division by zero" />
103 </stdio> 107 </stdio>
104 108
105 <help> 109 <help>
106 **What it does** 110 **What it does**
107 111