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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
author matthias
date Thu, 09 May 2019 16:32:37 -0400
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-1:000000000000 0:fce2e761129d
1 <tool id="mitos" name="MITOS" version="1.0.1">
2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3 <!--Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.-->
4 <edam_topics>
5 <edam_topic>topic_0114</edam_topic>
6 </edam_topics>
7 <!--Annotate a genome sequence with terms from a controlled vocabulary-->
8 <edam_operations>
9 <edam_operation>operation_0362</edam_operation>
10 </edam_operations>
11 <requirements>
12 <requirement type="package" version="1.0.1">mitos</requirement>
13 <requirement type="package">zip</requirement>
14 </requirements>
15 <version_command>python usage: %prog [options] --version</version_command>
16 <command detect_errors="aggressive"><![CDATA[
17 mkdir outdir &&
18
19 runmitos.py
20 --input '$input'
21 --code $code
22 --outdir outdir
23 --refdir /home/maze/workspace/mtdb/data/
24 #if not "prot" in $advanced.featuretypes
25 --noprot
26 #end if
27 #if not "trna" in $advanced.featuretypes
28 --notrna
29 #end if
30 #if not "rrna" in $advanced.featuretypes
31 --norrna
32 #end if
33 --finovl $advanced.finovl
34 --evalue $advanced_prot.evalue
35 --cutoff $advanced_prot.cutoff
36 #set maxovl=float($advanced_prot.maxovl)/100.0
37 --maxovl $maxovl
38 --clipfac $advanced_prot.clipfac
39 #set fragovl=float($advanced_prot.fragovl)/100.0
40 --fragovl $fragovl
41 --fragfac $advanced_prot.fragfac
42 --ststrange $advanced_prot.ststrange
43
44 #if "zip" in $outputs:
45 zip -9 -y -r output.zip output/"
46 #end if
47
48 ]]></command>
49 <inputs>
50 <param argument="--input" label="Sequences" optional="false" type="data" format="fasta"/>
51 <param argument="--code" label="Genetic code" name="code" type="select">
52 <option value="2">Vertebrate</option>
53 <option value="4">Mold, Protozoan, Coelenteral</option>
54 <option value="5">Invertebrate</option>
55 <option value="9">Echinoderm, Flatworm</option>
56 <option value="13">Ascidian</option>
57 <option value="14">Alternative Flatworm</option>
58 </param>
59 <section name="advanced" title="Advanced options">
60 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS" type="select" multiple="true">
61 <option value="prot" selected="true">Proteins</option>
62 <option value="trna" selected="true">tRNAs</option>
63 <option value="rrna" selected="true">rRNAs</option>
64 </param>
65 <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="35" min="0"/>
66 </section>
67 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
68 <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="0"/>
69 <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
70 <param argument="--maxovl" label="Maximum overlap" help="Maximum allowed overlap of proteins in percent of the smaller feature " type="integer" value="20" min="0" max="100"/>
71 <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
72 <param argument="--fragovl" label="Fragment overlap" help="Maximum allowed overlap of proteins in the query (in percent of the shorter query range) for two hits to be counted as fragments of the same gene" type="integer" value="20" min="0" max="100"/>
73 <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" value="10"/>
74 <param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
75 </section>
76 <param name="outputs" type="select" multiple="true" label="Additional outputs">
77 <option value="mito">mito</mito>
78 <option value="seq">SEQ</mito>
79 <option value="raw">zipped raw results</mito>
80 </param>
81 </inputs>
82 <outputs>
83 <data name="bedout" format="bed" from_work_dir="outdir/result.bed"/>
84 <data name="seqout" format="txt" from_work_dir="outdir/result.seq">
85 <filter>"seq" in outputs</filter>
86 </data>
87 <data name="mitoout" format="tabular" from_work_dir="outdir/result">
88 <filter>"mito" in outputs</filter>
89 </data>
90 <data name="rawout" format="zip" from_work_dir="outdir.zip">
91 <filter>"raw" in outputs</filter>
92 </data>
93 </outputs>
94 <help><![CDATA[
95 TODO: Write help
96 ]]></help>
97 <citations>
98 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
99 </citations>
100 </tool>
101