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comparison gotohscan.xml @ 0:6845ddcd5588 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit d18a08287799b0aa6ca50242ebcc218820923fb2-dirty
author rnateam
date Thu, 02 Jul 2015 12:06:30 -0400
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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 <stdio>
7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
9 </stdio>
10 <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
11 <command><![CDATA[
12 GotohScan
13
14 -d $dbase
15 -q $query
16
17 #if $split and $split is not None
18 --split $split
19 #end if
20
21 #if $e and $e is not None
22 -e $e
23 #end if
24
25 #if $p and $p is not None
26 -p $p
27 #end if
28
29 $s
30 -o $o
31 >
32
33 #if $o.value == '0'
34 $output0
35 #elif $o.value == '1'
36 $output1
37 #elif $o.value == '2'
38 $output2
39 #elif $o.value == '3'
40 $output3
41 #elif $o.value == '4'
42 $output4
43 #elif $o.value == '5'
44 $output5
45 #end if
46 ]]></command>
47 <inputs>
48 <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/>
49 <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
50 <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/>
51 <param argument="-e" name="e" type="float" optional="true" label="E-value" help="Value should be &lt; 10. default: 1e-3"/>
52 <param argument="-p" name="p" type="float" optional="true" label="Percent identity of aligned sequences" help="Value should be in [0.0,100.00]"/>
53 <param argument="-s" name="s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Print score distribution data for each query to a file"/>
54 <param argument="-o" name="o" type="select" label="Output Format">
55 <option value="0" selected="true">Blast tabular output</option>
56 <option value="1">Blast tabular output + aligned sequences</option>
57 <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option>
58 <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option>
59 <option value="4">BED + aligned sequences</option>
60 <option value="5">GFF + aligned sequences</option>
61 </param>
62 </inputs>
63 <outputs>
64 <data name="output0" format="tabular" label="${tool.name} on ${on_string}">
65 <filter>o == '0'</filter>
66 </data>
67 <data name="output1" format="tabular" label="${tool.name} on ${on_string}">
68 <filter>o == '1'</filter>
69 </data>
70 <data name="output2" format="fasta" label="${tool.name} on ${on_string}">
71 <filter>o == '2'</filter>
72 </data>
73 <data name="output3" format="maf" label="${tool.name} on ${on_string}">
74 <filter>o == '3'</filter>
75 </data>
76 <data name="output4" format="bed" label="${tool.name} on ${on_string}">
77 <filter>o == '4'</filter>
78 </data>
79 <data name="output5" format="gff" label="${tool.name} on ${on_string}">
80 <filter>o == '5'</filter>
81 </data>
82 </outputs>
83 <tests>
84 <test>
85 <param name="dbase" value="NC_000913.fna"/>
86 <param name="query" value="C0299.fa"/>
87 <param name="o" value="2"/>
88 <output name="" ftype="fasta" file="gotohscan.result1"/>
89 </test>
90 </tests>
91 <help>
92 <![CDATA[
93 **GotohScan** is a search tool that finds shorter sequences
94 (usually genes) in large database sequences (chromosomes, genomes, ..)
95 by computing all semi-global alignments. Thus, the query sequence is
96 never truncated or split into subsequences, but always mapped to the
97 database over its complete length. The alignment is computed via the
98 Gotoh-alignment algorithm using affine gap costs.
99 ]]></help>
100 <citations>
101 <citation type="doi">10.1093/nar/gkn1084</citation>
102 </citations>
103 </tool>