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comparison rgclustal/rgClustalw.xml @ 0:8888e4e3f169

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Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author fubar
date Tue, 07 Jun 2011 17:05:43 -0400
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-1:000000000000 0:8888e4e3f169
1 <tool id="clustalw" name="ClustalW" version="0.1">
2 <description>multiple sequence alignment program for DNA or proteins</description>
3 <command>
4 #if ($range.mode=="part")
5 clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order -RANGE=$range.seq_range_start,$range.seq_range_end
6 #elif ($range.mode=="complete")
7 clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order
8 #end if
9 #if ($outcontrol.outform=="clustal")
10 -SEQNOS=$outcontrol.out_seqnos
11 #end if
12 #if ($outcontrol.outform=="phylip")
13 -OUTPUT=PHYLIP
14 #end if
15 #if ($outcontrol.outform=="fasta")
16 -OUTPUT=FASTA
17 #end if
18 -TYPE=$dnarna 1&gt;$outlog 2&gt;&amp;1
19 </command>
20 <inputs>
21 <page>
22 <param format="fasta" name="input" type="data" label="Fasta File" />
23 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" size="50" value="Clustal_run" />
24 <param name="dnarna" type="select" label="Data Type">
25 <option value="DNA" selected="True">DNA nucleotide sequences</option>
26 <option value="PROTEIN">Protein sequences</option>
27 </param>
28 <conditional name="outcontrol">
29 <param name="outform" type="select" label="Output alignment format">
30 <option value="clustal" selected="True">Native Clustal output format</option>
31 <option value="phylip">Phylip format</option>
32 <option value="fasta">Fasta format</option>
33 </param>
34 <when value="fasta" />
35 <when value="phylip" />
36 <when value="clustal">
37 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output">
38 <option value="ON">yes</option>
39 <option value="OFF" selected="true">no</option>
40 </param>
41 </when>
42 </conditional>
43 <param name="out_order" type="select" label="Output Order">
44 <option value="ALIGNED">aligned</option>
45 <option value="INPUT">same order as input file</option>
46 </param>
47
48 <conditional name="range">
49 <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
50 <option value="complete">complete alignment</option>
51 <option value="part">only part of the alignment</option>
52 </param>
53 <when value="complete">
54 </when>
55 <when value="part">
56 <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write">
57 </param>
58 <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" >
59 </param>
60 </when>
61 </conditional>
62 </page>
63 </inputs>
64 <outputs>
65 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}">
66 <change_format>
67 <when input="outcontrol.outform" value="phylip" format="phylip" />
68 <when input="outcontrol.outform" value="fasta" format="fasta" />
69 </change_format>
70 </data>
71 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/>
72 </outputs>
73 <tests>
74 <test>
75 <param name="input" value="rgClustal_testin.fasta" />
76 <param name = "outname" value="" />
77 <param name = "outform" value="fasta" />
78 <param name = "dnarna" value="DNA" />
79 <param name = "mode" value="complete" />
80 <param name = "out_order" value="ALIGNED" />
81 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
82 <output name="output" file="rgClustal_testout.log" ftype="txt" lines_diff="5" />
83 </test>
84 </tests>
85 <help>
86
87 **Note**
88
89 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options.
90
91 For a tutorial introduction, see ClustalW2_
92
93 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file
94
95 A log will be output to your history showing the output Clustal would normally write to standard output.
96
97 The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history. If you choose fasta as
98 the output format, you can create a 'Logo' image using the Sequence Logo tool.
99
100 If Clustal format is chosen, you have the option of adding basepair counts to the output
101
102 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output
103
104 ----
105
106 **Attribution**
107
108 Clustal attribution and associated documentation are available at Clustsrc_
109
110 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_
111
112 It was modified by Ross Lazarus for the rgenetics project
113
114 This wrapper is now LGPL
115
116 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html
117
118 .. _Clustsrc: http://www.clustal.org
119
120 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
121
122 </help>
123
124 </tool>
125