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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867
author rnateam
date Sun, 12 Nov 2017 18:17:28 -0500
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-1:000000000000 0:7c534a070e7e
1 <tool id="rbc_gotohscan" name="GotohScan" version="1.3.0">
2 <description>Find subsequences in db</description>
3 <requirements>
4 <requirement type="package" version="1.3">gotohscan</requirement>
5 </requirements>
6 <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 GotohScan
9 -d '$dbase'
10 -q '$query'
11
12 #if $split
13 --split $split
14 #end if
15
16 #if $e
17 -e $e
18 #end if
19
20 #if $p
21 -p $p
22 #end if
23
24 $s
25 -o $o
26 >
27
28 #if $o.value == '0'
29 '$output0'
30 #elif $o.value == '1'
31 '$output1'
32 #elif $o.value == '2'
33 '$output2'
34 #elif $o.value == '3'
35 '$output3'
36 #elif $o.value == '4'
37 '$output4'
38 #elif $o.value == '5'
39 '$output5'
40 #end if
41 ]]></command>
42 <inputs>
43 <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/>
44 <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
45 <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/>
46 <param argument="-e" name="e" type="float" optional="true" label="E-value" help="Value should be &lt; 10. default: 1e-3"/>
47 <param argument="-p" name="p" type="float" optional="true" label="Percent identity of aligned sequences" help="Value should be in [0.0,100.00]"/>
48 <param argument="-s" name="s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Print score distribution data for each query to a file"/>
49 <param argument="-o" name="o" type="select" label="Output Format">
50 <option value="0" selected="true">Blast tabular output</option>
51 <option value="1">Blast tabular output + aligned sequences</option>
52 <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option>
53 <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option>
54 <option value="4">BED + aligned sequences</option>
55 <option value="5">GFF + aligned sequences</option>
56 </param>
57 </inputs>
58 <outputs>
59 <data name="output0" format="tabular" label="${tool.name} on ${on_string}">
60 <filter>o == '0'</filter>
61 </data>
62 <data name="output1" format="tabular" label="${tool.name} on ${on_string}">
63 <filter>o == '1'</filter>
64 </data>
65 <data name="output2" format="fasta" label="${tool.name} on ${on_string}">
66 <filter>o == '2'</filter>
67 </data>
68 <data name="output3" format="maf" label="${tool.name} on ${on_string}">
69 <filter>o == '3'</filter>
70 </data>
71 <data name="output4" format="bed" label="${tool.name} on ${on_string}">
72 <filter>o == '4'</filter>
73 </data>
74 <data name="output5" format="gff" label="${tool.name} on ${on_string}">
75 <filter>o == '5'</filter>
76 </data>
77 </outputs>
78 <tests>
79 <test>
80 <param name="dbase" value="NC_000913.fna"/>
81 <param name="query" value="C0299.fa"/>
82 <param name="o" value="2"/>
83 <output name="" ftype="fasta" file="gotohscan.result1"/>
84 </test>
85 </tests>
86 <help>
87 <![CDATA[
88
89 **GotohScan** is a search tool that finds shorter sequences
90 (usually genes) in large database sequences (chromosomes, genomes, ..)
91 by computing all semi-global alignments. Thus, the query sequence is
92 never truncated or split into subsequences, but always mapped to the
93 database over its complete length. The alignment is computed via the
94 Gotoh-alignment algorithm using affine gap costs.
95
96 ]]></help>
97 <citations>
98 <citation type="doi">10.1093/nar/gkn1084</citation>
99 </citations>
100 </tool>