Mercurial > repos > lionelguy > prokka
comparison prokka.xml @ 3:5c289bf13a08 draft
Uploaded
author | lionelguy |
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date | Thu, 05 Sep 2013 03:59:23 -0400 |
parents | 2bb7c28ea68f |
children | 39bc9c61c55b |
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2:bb07951d72db | 3:5c289bf13a08 |
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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 |