Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 8:756376aeb1ae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 1102ae206f5dfb9322d28b23d224eb67a7b80a1c
author iuc
date Wed, 01 Nov 2023 09:52:58 +0000
parents b6b5cd37f2a2
children 3bbe70fef6df
comparison
equal deleted inserted replaced
7:b6b5cd37f2a2 8:756376aeb1ae
1 <tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>annotation</description> 2 <description>annotation</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>funannotate check --show-versions</version_command> 10 <version_command>funannotate check --show-versions</version_command>
10 <command><![CDATA[ 11 <command><![CDATA[
64 --fix '${fix}' 65 --fix '${fix}'
65 #end if 66 #end if
66 #if $remove: 67 #if $remove:
67 --remove '${remove}' 68 --remove '${remove}'
68 #end if 69 #end if
69 70 --header_length $header_length
70 --cpus \${GALAXY_SLOTS:-2} 71 --cpus \${GALAXY_SLOTS:-2}
71 72
72 && 73 &&
73 74
74 ## funannotate sometimes leaves multiple *part.tbl and *part.sqn files 75 ## funannotate sometimes leaves multiple *part.tbl and *part.sqn files
110 <validator type="empty_field" /> 111 <validator type="empty_field" />
111 </param> 112 </param>
112 </when> 113 </when>
113 </conditional> 114 </conditional>
114 115
115
116
117 <param name="database" label="Funannotate database" type="select"> 116 <param name="database" label="Funannotate database" type="select">
118 <options from_data_table="funannotate"> 117 <options from_data_table="funannotate">
119 <column name="value" index="0" /> 118 <column name="value" index="0" />
120 <column name="name" index="1" /> 119 <column name="name" index="1" />
121 <column name="path" index="3" /> 120 <column name="path" index="3" />
142 141
143 <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" /> 142 <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" />
144 <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID Name Product" /> 143 <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID Name Product" />
145 <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene Product" /> 144 <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene Product" />
146 145
146 <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." />
147 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 147 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
148 <option value="gbk" selected="true">Annotated genome (genbank)</option> 148 <option value="gbk" selected="true">Annotated genome (genbank)</option>
149 <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option> 149 <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>
150 <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option> 150 <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option>
151 <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option> 151 <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option>