Mercurial > repos > genouest > braker

comparison braker.xml @ 0:e50ea151f221 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
author genouest
date Tue, 05 Oct 2021 12:35:42 +0000
parents
children ca7c12566894
comparison
equal deleted inserted replaced
-1:000000000000 0:e50ea151f221
1 <tool id="braker" name="Braker genome annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <expand macro="requirements" />
8 </requirements>
9 <version_command><![CDATA[braker.pl --version; $GENEMARK_PATH/gmes_petap.pl | grep version]]></version_command>
10 <command><![CDATA[
11 if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&
12 if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&
13 ## GeneMark only search for license in ~/.gm_key
14 cp '${genemark_license}' ~/.gm_key &&
15
16 braker.pl
17 --genome '${genome}'
18
19 $softmasking
20
21 #if $evidences.bam:
22 --bam ${evidences.bam}
23 #end if
24
25 #if $evidences.prot_seq:
26 --prot_seq ${evidences.prot_seq}
27 #end if
28
29 ## No hints, use esmode
30 #if not $evidences.bam and not $evidences.prot_seq
31 --esmode
32 #end if
33
34 #if $output_format == 'gff3'
35 --gff3
36 #end if
37
38 $genemark.fungus
39
40 $augustus.crf
41 --rounds $augustus.rounds
42
43 $advanced.UTR
44
45 $advanced.filterOutShort
46
47 #if $advanced.eval:
48 --eval ${advanced.eval}
49 #end if
50
51 #if $advanced.eval_pseudo:
52 --eval_pseudo ${advanced.eval_pseudo}
53 #end if
54
55 --cores \${GALAXY_SLOTS:-2}
56 ]]></command>
57 <inputs>
58 <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." />
59
60 <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should be soft-masked (with RepeatMasker for example)" />
61
62 <param argument="--softmasking" type="boolean" checked="false" truevalue="--softmasking" falsevalue="" label="Genome sequence is soft-masked" />
63
64 <section name="evidences" expanded="true" title="Evidences">
65 <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" />
66 <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" />
67 </section>
68
69 <section name="genemark" expanded="true" title="GeneMark">
70 <param argument="--fungus" type="boolean" checked="false" truevalue="--fungus" falsevalue="" label="Fungal genome" help="GeneMark-EX option, run algorithm with branch point model (most useful for fungal genomes)" />
71 </section>
72
73 <section name="augustus" expanded="true" title="Augustus">
74 <param argument="--crf" type="boolean" checked="false" truevalue="--crf" falsevalue="" label="Use CRF training for Augustus" help="Alternate training method (Conditional Random Field)" />
75 <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" />
76 </section>
77
78 <section name="advanced" expanded="false" title="Advanced">
79 <param argument="--UTR" type="boolean" checked="false" truevalue="--UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" />
80 <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short traingin gene predicted by GeneMark-EX" />
81 <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" />
82 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" />
83 </section>
84
85 <param name="output_format" type="select" label="Output format">
86 <option value="gtf" selected="true">GTF</option>
87 <option value="gff3">GFF3</option>
88 </param>
89 </inputs>
90 <outputs>
91 <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gtf">
92 <filter>output_format == 'gtf'</filter>
93 </data>
94 <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gff3">
95 <filter>output_format == 'gff3'</filter>
96 </data>
97 </outputs>
98 <tests>
99 <!-- Disable next 2 for CI (it should pass locally)-->
100 <!--test>
101 <param name="genome" value="genome_masked.fa" />
102 <param name="softmasking" value="true" />
103 <param name="genemark_license" value="genemark_license.gm_key" />
104 <output name="output_gtf" file="out_genome/braker.gtf" sort="true" />
105 </test>
106 <test>
107 <param name="genome" value="genome_masked.fa" />
108 <param name="softmasking" value="true" />
109 <param name="genemark_license" value="genemark_license.gm_key" />
110 <param name="output_format" value="gff3" />
111 <output name="output_gff" file="out_genome/braker.gff3" sort="true" />
112 </test-->
113 <!-- following 2 tests throw an error because test dataset is too small -->
114 <!--test>
115 <param name="genome" value="genome_masked.fa" />
116 <param name="softmasking" value="true" />
117 <param name="genemark_license" value="genemark_license.gm_key" />
118 <section name="evidences">
119 <param name="bam" value="SRR7458692.bam" />
120 </section>
121 <output name="output_gtf" file="out_bam/braker.gtf" sort="true" />
122 </test>
123 <test>
124 <param name="genome" value="genome_masked.fa" />
125 <param name="softmasking" value="true" />
126 <param name="genemark_license" value="genemark_license.gm_key" />
127 <section name="evidences">
128 <param name="prot_seq" value="proteins.fa" />
129 </section>
130 <output name="output_gtf" file="out_prot/braker.gtf" sort="true" />
131 </test-->
132 </tests>
133 <help><![CDATA[
134 Braker_
135 -------
136
137 Braker_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
138
139 In contrast to other available methods that rely on protein homology information, BRAKER reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.
140
141 .. _Braker: https://github.com/Gaius-Augustus/BRAKER
142 ]]></help>
143 <expand macro="citations" />
144 </tool>