Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 2:a1a3f92159f7 draft

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"planemo upload commit 9cbeba115a6e13dd4c007065b7d77dcb400f72fb"
author iuc
date Thu, 25 Nov 2021 09:37:41 +0000
parents 5802296edf11
children cb06fd12e746
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1:231be78ca278 2:a1a3f92159f7
6 <requirements> 6 <requirements>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 </requirements> 8 </requirements>
9 <version_command>funannotate check --show-versions</version_command> 9 <version_command>funannotate check --show-versions</version_command>
10 <command><![CDATA[ 10 <command><![CDATA[
11
12 #if $uglyTestingHack == "true":
13 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
14 ## Need to copy too as the test_data is read only on CI
15 cp -r '${database.fields.path}' './hacked_database' &&
16 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
17 #end if
18
19 funannotate annotate 11 funannotate annotate
20 12
21 #if $input.input_type == 'gbk' 13 #if $input.input_type == 'gbk'
22 --genbank '${input.genbank}' 14 --genbank '${input.genbank}'
23 #else 15 #else
26 --species '${input.species}' 18 --species '${input.species}'
27 #end if 19 #end if
28 20
29 --out output 21 --out output
30 22
31 #if $uglyTestingHack == "true": 23 --database '$database.fields.path'
32 --database `pwd`'/hacked_database'
33 #else
34 --database '$database.fields.path'
35 #end if
36 24
37 #if $sbt: 25 #if $sbt:
38 --sbt '${sbt}' 26 --sbt '${sbt}'
39 #end if 27 #end if
40 28
120 <filter type="sort_by" column="0" /> 108 <filter type="sort_by" column="0" />
121 <filter type="static_value" column="2" value="1.0" /> 109 <filter type="static_value" column="2" value="1.0" />
122 </options> 110 </options>
123 </param> 111 </param>
124 112
125 <param argument="--sbt" type="data" format="sbt" 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)" /> 113 <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)" />
126 114
127 <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" /> 115 <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" />
128 <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" /> 116 <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" />
129 <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" /> 117 <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" />
130 <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" /> 118 <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" />
158 <option value="stats">Statistics</option> 146 <option value="stats">Statistics</option>
159 <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option> 147 <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option>
160 <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option> 148 <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
161 <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option> 149 <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
162 </param> 150 </param>
163
164 <!-- Need this to change path in the test funannotate_db -->
165 <param type="hidden" name="uglyTestingHack" value="" />
166 </inputs> 151 </inputs>
167 <outputs> 152 <outputs>
168 <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk"> 153 <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">
169 <filter>outputs and 'gbk' in outputs</filter> 154 <filter>outputs and 'gbk' in outputs</filter>
170 </data> 155 </data>