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comparison gotohscan.xml @ 1:c172fed9eb75 draft default tip

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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 06:10:23 -0500
parents 6845ddcd5588
children
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0:6845ddcd5588 1:c172fed9eb75
1 <tool id="rbc_gotohscan" name="GotohScan" version="1.3.0"> 1 <tool id="rbc_gotohscan" name="GotohScan" version="1.3.0">
2 <description>Find subsequences in db</description> 2 <description>Find subsequences in db</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3">gotohscan</requirement> 4 <requirement type="package" version="1.3">gotohscan</requirement>
5 </requirements> 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> 6 <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
11 <command><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
12 GotohScan 8 GotohScan
9 -d '$dbase'
10 -q '$query'
13 11
14 -d $dbase 12 #if $split
15 -q $query
16
17 #if $split and $split is not None
18 --split $split 13 --split $split
19 #end if 14 #end if
20 15
21 #if $e and $e is not None 16 #if $e
22 -e $e 17 -e $e
23 #end if 18 #end if
24 19
25 #if $p and $p is not None 20 #if $p
26 -p $p 21 -p $p
27 #end if 22 #end if
28 23
29 $s 24 $s
30 -o $o 25 -o $o
31 > 26 >
32 27
33 #if $o.value == '0' 28 #if $o.value == '0'
34 $output0 29 '$output0'
35 #elif $o.value == '1' 30 #elif $o.value == '1'
36 $output1 31 '$output1'
37 #elif $o.value == '2' 32 #elif $o.value == '2'
38 $output2 33 '$output2'
39 #elif $o.value == '3' 34 #elif $o.value == '3'
40 $output3 35 '$output3'
41 #elif $o.value == '4' 36 #elif $o.value == '4'
42 $output4 37 '$output4'
43 #elif $o.value == '5' 38 #elif $o.value == '5'
44 $output5 39 '$output5'
45 #end if 40 #end if
46 ]]></command> 41 ]]></command>
47 <inputs> 42 <inputs>
48 <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/> 43 <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"/> 44 <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
88 <output name="" ftype="fasta" file="gotohscan.result1"/> 83 <output name="" ftype="fasta" file="gotohscan.result1"/>
89 </test> 84 </test>
90 </tests> 85 </tests>
91 <help> 86 <help>
92 <![CDATA[ 87 <![CDATA[
88
93 **GotohScan** is a search tool that finds shorter sequences 89 **GotohScan** is a search tool that finds shorter sequences
94 (usually genes) in large database sequences (chromosomes, genomes, ..) 90 (usually genes) in large database sequences (chromosomes, genomes, ..)
95 by computing all semi-global alignments. Thus, the query sequence is 91 by computing all semi-global alignments. Thus, the query sequence is
96 never truncated or split into subsequences, but always mapped to the 92 never truncated or split into subsequences, but always mapped to the
97 database over its complete length. The alignment is computed via the 93 database over its complete length. The alignment is computed via the
98 Gotoh-alignment algorithm using affine gap costs. 94 Gotoh-alignment algorithm using affine gap costs.
95
99 ]]></help> 96 ]]></help>
100 <citations> 97 <citations>
101 <citation type="doi">10.1093/nar/gkn1084</citation> 98 <citation type="doi">10.1093/nar/gkn1084</citation>
102 </citations> 99 </citations>
103 </tool> 100 </tool>