Mercurial > repos > iuc > funannotate_predict

comparison funannotate_predict.xml @ 10:1bc5a03faf2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 1102ae206f5dfb9322d28b23d224eb67a7b80a1c
author iuc
date Wed, 01 Nov 2023 09:53:49 +0000
parents d6c7106b7b2e
children 4b96ced19f75
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9:d6c7106b7b2e 10:1bc5a03faf2e
1 <tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools" />
6 <requirements> 7 <requirements>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 </requirements> 9 </requirements>
9 <version_command><![CDATA[funannotate check --show-versions]]></version_command> 10 <version_command><![CDATA[funannotate check --show-versions]]></version_command>
10 <command><![CDATA[ 11 <command><![CDATA[
43 --ploidy ${organism.ploidy} 44 --ploidy ${organism.ploidy}
44 --SeqCenter '${organism.SeqCenter}' 45 --SeqCenter '${organism.SeqCenter}'
45 --SeqAccession '${organism.SeqAccession}' 46 --SeqAccession '${organism.SeqAccession}'
46 --name '${organism.name}' 47 --name '${organism.name}'
47 --numbering ${organism.numbering} 48 --numbering ${organism.numbering}
49 --header_length ${header_length}
48 50
49 #if $parameters: 51 #if $parameters:
50 --parameters '${parameters}' 52 --parameters '${parameters}'
51 #end if 53 #end if
52 54
251 </conditional> 253 </conditional>
252 <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10"> 254 <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10">
253 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator> 255 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
254 </param> 256 </param>
255 </section> 257 </section>
256 258 <param argument="--header_length" type="integer" value="16" min="1" label="Maximum length of FASTA headers" help="The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI." />
257 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 259 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
258 <option value="gbk" selected="true">Annotated genome (genbank)</option> 260 <option value="gbk" selected="true">Annotated genome (genbank)</option>
259 <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option> 261 <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
260 <option value="gff3">Annotation in GFF3 format</option> 262 <option value="gff3">Annotation in GFF3 format</option>
261 <option value="proteins_fa">Multi-fasta file of protein coding genes</option> 263 <option value="proteins_fa">Multi-fasta file of protein coding genes</option>