Mercurial > repos > xuebing > sharplabtool
comparison tools/rgenetics/rgClustalw.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9071e359b9a3 |
---|---|
1 <tool id="clustalw" name="ClustalW" version="0.1"> | |
2 <description>multiple sequence alignment program for DNA or proteins</description> | |
3 <command interpreter="python"> | |
4 rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" | |
5 #if ($range.mode=="part") | |
6 -b "$range.seq_range_start" -e "$range.seq_range_end" | |
7 #end if | |
8 #if ($outcontrol.outform=="clustal") | |
9 -f "CLUSTAL" | |
10 #if ($outcontrol.out_seqnos=="ON") | |
11 -q "ON" | |
12 #end if | |
13 #end if | |
14 #if ($outcontrol.outform=="phylip") | |
15 -f "PHYLIP" | |
16 #end if | |
17 #if ($outcontrol.outform=="fasta") | |
18 -f "FASTA" | |
19 #end if | |
20 </command> | |
21 <inputs> | |
22 <page> | |
23 <param format="fasta" name="input" type="data" label="Fasta File" /> | |
24 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" size="50" value="Clustal_run" /> | |
25 <param name="dnarna" type="select" label="Data Type"> | |
26 <option value="DNA" selected="True">DNA nucleotide sequences</option> | |
27 <option value="PROTEIN">Protein sequences</option> | |
28 </param> | |
29 <conditional name="outcontrol"> | |
30 <param name="outform" type="select" label="Output alignment format"> | |
31 <option value="clustal" selected="True">Native Clustal output format</option> | |
32 <option value="phylip">Phylip format</option> | |
33 <option value="fasta">Fasta format</option> | |
34 </param> | |
35 <when value="fasta" /> | |
36 <when value="phylip" /> | |
37 <when value="clustal"> | |
38 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output"> | |
39 <option value="ON">yes</option> | |
40 <option value="OFF" selected="true">no</option> | |
41 </param> | |
42 </when> | |
43 </conditional> | |
44 <param name="out_order" type="select" label="Output Order"> | |
45 <option value="ALIGNED">aligned</option> | |
46 <option value="INPUT">same order as input file</option> | |
47 </param> | |
48 | |
49 <conditional name="range"> | |
50 <param name="mode" type="select" label="Output complete alignment (or specify part to output)"> | |
51 <option value="complete">complete alignment</option> | |
52 <option value="part">only part of the alignment</option> | |
53 </param> | |
54 <when value="complete"> | |
55 </when> | |
56 <when value="part"> | |
57 <param name="seq_range_start" size="5" type="integer" value="1" label="start point" help="sequence range to write"> | |
58 </param> | |
59 <param name="seq_range_end" size="5" type="integer" value="99999" label="end point" > | |
60 </param> | |
61 </when> | |
62 </conditional> | |
63 </page> | |
64 </inputs> | |
65 <outputs> | |
66 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}"> | |
67 <change_format> | |
68 <when input="outcontrol.outform" value="phylip" format="phylip" /> | |
69 <when input="outcontrol.outform" value="fasta" format="fasta" /> | |
70 </change_format> | |
71 </data> | |
72 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/> | |
73 </outputs> | |
74 <tests> | |
75 <test> | |
76 <param name="input" value="rgClustal_testin.fasta" /> | |
77 <param name = "outname" value="" /> | |
78 <param name = "outform" value="fasta" /> | |
79 <param name = "dnarna" value="DNA" /> | |
80 <param name = "mode" value="complete" /> | |
81 <param name = "out_order" value="ALIGNED" /> | |
82 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> | |
83 <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> | |
84 </test> | |
85 </tests> | |
86 <help> | |
87 | |
88 **Note** | |
89 | |
90 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options. | |
91 | |
92 For a tutorial introduction, see ClustalW2_ | |
93 | |
94 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file | |
95 | |
96 A log will be output to your history showing the output Clustal would normally write to standard output. | |
97 | |
98 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 | |
99 the output format, you can create a 'Logo' image using the Sequence Logo tool. | |
100 | |
101 If Clustal format is chosen, you have the option of adding basepair counts to the output | |
102 | |
103 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 | |
104 | |
105 ---- | |
106 | |
107 **Attribution** | |
108 | |
109 Clustal attribution and associated documentation are available at Clustsrc_ | |
110 | |
111 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ | |
112 | |
113 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added | |
114 | |
115 This wrapper is released licensed under the LGPL_ | |
116 | |
117 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html | |
118 | |
119 .. _Clustsrc: http://www.clustal.org | |
120 | |
121 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html | |
122 | |
123 .. _LGPL: http://www.gnu.org/copyleft/lesser.html | |
124 | |
125 </help> | |
126 | |
127 </tool> | |
128 |