Mercurial > repos > iuc > snap
comparison snap.xml @ 0:d398b2e6b2ff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author | iuc |
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date | Fri, 20 Oct 2017 03:52:36 -0400 |
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-1:000000000000 | 0:d398b2e6b2ff |
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1 <tool id="snap" name="SNAP" profile="16.04" version="@VERSION@"> | |
2 <description>gene prediction</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 snap | |
9 -gff | |
10 $lcmask | |
11 #if $strand == 'forward' | |
12 -plus | |
13 #else if $strand == 'backward' | |
14 -minus | |
15 #end if | |
16 -aa '${output_aa}' | |
17 -tx '${output_tx}' | |
18 '${model}' | |
19 '${input_genome}' | |
20 > '${output_gff}' | |
21 ]]> | |
22 </command> | |
23 <inputs> | |
24 <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> | |
25 | |
26 <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/> | |
27 | |
28 <param argument="-lcmask" type="boolean" | |
29 label="Treat lowercase as N" | |
30 truevalue="-lcmask" falsevalue="" checked="false" /> | |
31 | |
32 <param name="strand" type="select" | |
33 label="Predict genes on specific strands"> | |
34 <option value="both">both</option> | |
35 <option value="forward">forward</option> | |
36 <option value="backward">backward</option> | |
37 </param> | |
38 </inputs> | |
39 <outputs> | |
40 <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/> | |
41 <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/> | |
42 <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/> | |
43 </outputs> | |
44 <tests> | |
45 <test> | |
46 <param name="input_genome" value="human.fa" ftype="fasta" /> | |
47 <param name="model" value="snap.hmm" /> | |
48 <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests --> | |
49 <!--param name="model" value="snap.hmm" ftype="snaphmm" /--> | |
50 <output name="output_gff" file="snap_annot.gff" ftype="gff"/> | |
51 <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/> | |
52 <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/> | |
53 </test> | |
54 </tests> | |
55 <help> | |
56 <![CDATA[ | |
57 SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. | |
58 ]]> | |
59 </help> | |
60 <expand macro="citations"/> | |
61 </tool> |