Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 8:51ca9670dcd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author iuc
date Fri, 07 Mar 2025 22:31:16 +0000
parents f6482e570d32
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7:f6482e570d32 8:51ca9670dcd1
9 </requirements> 9 </requirements>
10 <version_command>funannotate check --show-versions</version_command> 10 <version_command>funannotate check --show-versions</version_command>
11 <command><![CDATA[ 11 <command><![CDATA[
12 ## Needed by some subprocess invoked internally 12 ## Needed by some subprocess invoked internally
13 ## https://github.com/nextgenusfs/funannotate/issues/905 13 ## https://github.com/nextgenusfs/funannotate/issues/905
14 export FUNANNOTATE_DB='$database.fields.path' 14 export FUNANNOTATE_DB='$database.fields.path' &&
15 15
16 && 16 ## show detailed info about the reference DB on stdout
17 funannotate database &&
17 18
18 funannotate annotate 19 funannotate annotate
19 20
20 #if $input.input_type == 'gbk' 21 #if $input.input_type == 'gbk'
21 --genbank '${input.genbank}' 22 --genbank '${input.genbank}'
104 <param name="database" label="Funannotate database" type="select"> 105 <param name="database" label="Funannotate database" type="select">
105 <options from_data_table="funannotate"> 106 <options from_data_table="funannotate">
106 <column name="value" index="0" /> 107 <column name="value" index="0" />
107 <column name="name" index="1" /> 108 <column name="name" index="1" />
108 <column name="path" index="3" /> 109 <column name="path" index="3" />
109 <filter type="sort_by" column="0" /> 110 <filter type="sort_by" column="0" reverse_sort_order="true"/>
110 <filter type="static_value" column="2" value="1.0" /> 111 <filter type="static_value" column="2" value="1.0" />
111 </options> 112 </options>
112 </param> 113 </param>
113 114
114 <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" /> 115 <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />