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comparison rgclustal/rgClustalw.xml @ 3:9c4d943fbef7 draft default tip

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author fubar
date Sun, 01 Dec 2013 20:07:58 -0500
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1 <tool id="clustalw" name="ClustalW" version="0.2">
2 <description>multiple sequence alignment program for DNA or proteins</description>
3 <requirements>
4 <requirement type="package" version="2.1">clustalw</requirement>
5 </requirements>
6 <command>
7 #if ($range.mode=="part")
8 clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order -RANGE=$range.seq_range_start,$range.seq_range_end
9 #elif ($range.mode=="complete")
10 clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order
11 #end if
12 #if ($outcontrol.outform=="clustal")
13 -SEQNOS=$outcontrol.out_seqnos
14 #end if
15 #if ($outcontrol.outform=="phylip")
16 -OUTPUT=PHYLIP
17 #end if
18 #if ($outcontrol.outform=="fasta")
19 -OUTPUT=FASTA
20 #end if
21 -TYPE=$dnarna 1&gt;$outlog 2&gt;&amp;1
22 </command>
23 <inputs>
24 <page>
25 <param format="fasta" name="input" type="data" label="Fasta File" />
26 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" size="50" value="Clustal_run" />
27 <param name="dnarna" type="select" label="Data Type">
28 <option value="DNA" selected="True">DNA nucleotide sequences</option>
29 <option value="PROTEIN">Protein sequences</option>
30 </param>
31 <conditional name="outcontrol">
32 <param name="outform" type="select" label="Output alignment format">
33 <option value="clustal" selected="True">Native Clustal output format</option>
34 <option value="phylip">Phylip format</option>
35 <option value="fasta">Fasta format</option>
36 </param>
37 <when value="fasta" />
38 <when value="phylip" />
39 <when value="clustal">
40 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output">
41 <option value="ON">yes</option>
42 <option value="OFF" selected="true">no</option>
43 </param>
44 </when>
45 </conditional>
46 <param name="out_order" type="select" label="Output Order">
47 <option value="ALIGNED">aligned</option>
48 <option value="INPUT">same order as input file</option>
49 </param>
50
51 <conditional name="range">
52 <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
53 <option value="complete">complete alignment</option>
54 <option value="part">only part of the alignment</option>
55 </param>
56 <when value="complete">
57 </when>
58 <when value="part">
59 <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write">
60 </param>
61 <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" >
62 </param>
63 </when>
64 </conditional>
65 </page>
66 </inputs>
67 <outputs>
68 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}">
69 <change_format>
70 <when input="outcontrol.outform" value="phylip" format="phylip" />
71 <when input="outcontrol.outform" value="fasta" format="fasta" />
72 </change_format>
73 </data>
74 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/>
75 </outputs>
76 <tests>
77 <test>
78 <param name="input" value="rgClustal_testin.fasta" />
79 <param name = "outname" value="" />
80 <param name = "outform" value="fasta" />
81 <param name = "dnarna" value="DNA" />
82 <param name = "mode" value="complete" />
83 <param name = "out_order" value="ALIGNED" />
84 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
85 <output name="output" file="rgClustal_testout.log" ftype="txt" lines_diff="5" />
86 </test>
87 </tests>
88 <help>
89
90 **Note**
91
92 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options.
93
94 For a tutorial introduction, see ClustalW2_
95
96 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file
97
98 A log will be output to your history showing the output Clustal would normally write to standard output.
99
100 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
101 the output format, you can create a 'Logo' image using the Sequence Logo tool.
102
103 If Clustal format is chosen, you have the option of adding basepair counts to the output
104
105 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
106
107 ----
108
109 **Attribution**
110
111 Clustal attribution and associated documentation are available at Clustsrc_
112
113 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_
114
115 It was modified by Ross Lazarus for the rgenetics project
116
117 This wrapper is now LGPL
118
119 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html
120
121 .. _Clustsrc: http://www.clustal.org
122
123 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
124
125 </help>
126
127 </tool>
128