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annotate rgClustalw.xml @ 1:ce785326df6e draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:14:40 -0400 |
parents | de3662385a52 |
children | bed27b5c0f63 |
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0 | 1 <tool id="clustalw" name="ClustalW" version="0.1"> |
2 <requirements> | |
3 <requirement type="package" version="2.1">clustalw2</requirement> | |
4 </requirements> | |
5 <description>multiple sequence alignment program for DNA or proteins</description> | |
6 <command interpreter="python"> | |
7 rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" | |
8 #if ($range.mode=="part") | |
9 -b "$range.seq_range_start" -e "$range.seq_range_end" | |
10 #end if | |
11 #if ($outcontrol.outform=="clustal") | |
12 -f "CLUSTAL" | |
13 #if ($outcontrol.out_seqnos=="ON") | |
14 -q "ON" | |
15 #end if | |
16 #end if | |
17 #if ($outcontrol.outform=="phylip") | |
18 -f "PHYLIP" | |
19 #end if | |
20 #if ($outcontrol.outform=="fasta") | |
21 -f "FASTA" | |
22 #end if | |
23 </command> | |
24 <inputs> | |
25 <page> | |
26 <param format="fasta" name="input" type="data" label="Fasta File" /> | |
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27 <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" value="Clustal_run" /> |
0 | 28 <param name="dnarna" type="select" label="Data Type"> |
29 <option value="DNA" selected="True">DNA nucleotide sequences</option> | |
30 <option value="PROTEIN">Protein sequences</option> | |
31 </param> | |
32 <conditional name="outcontrol"> | |
33 <param name="outform" type="select" label="Output alignment format"> | |
34 <option value="clustal" selected="True">Native Clustal output format</option> | |
35 <option value="phylip">Phylip format</option> | |
36 <option value="fasta">Fasta format</option> | |
37 </param> | |
38 <when value="fasta" /> | |
39 <when value="phylip" /> | |
40 <when value="clustal"> | |
41 <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output"> | |
42 <option value="ON">yes</option> | |
43 <option value="OFF" selected="true">no</option> | |
44 </param> | |
45 </when> | |
46 </conditional> | |
47 <param name="out_order" type="select" label="Output Order"> | |
48 <option value="ALIGNED">aligned</option> | |
49 <option value="INPUT">same order as input file</option> | |
50 </param> | |
51 | |
52 <conditional name="range"> | |
53 <param name="mode" type="select" label="Output complete alignment (or specify part to output)"> | |
54 <option value="complete">complete alignment</option> | |
55 <option value="part">only part of the alignment</option> | |
56 </param> | |
57 <when value="complete"> | |
58 </when> | |
59 <when value="part"> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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60 <param name="seq_range_start" type="integer" value="1" label="start point" help="sequence range to write"> |
0 | 61 </param> |
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ce785326df6e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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62 <param name="seq_range_end" type="integer" value="99999" label="end point" > |
0 | 63 </param> |
64 </when> | |
65 </conditional> | |
66 </page> | |
67 </inputs> | |
68 <outputs> | |
69 <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}"> | |
70 <change_format> | |
71 <when input="outcontrol.outform" value="phylip" format="phylip" /> | |
72 <when input="outcontrol.outform" value="fasta" format="fasta" /> | |
73 </change_format> | |
74 </data> | |
75 <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/> | |
76 </outputs> | |
77 <tests> | |
78 <test> | |
79 <param name="input" value="rgClustal_testin.fasta" /> | |
80 <param name="outname" value="" /> | |
81 <param name="outform" value="fasta" /> | |
82 <param name="dnarna" value="DNA" /> | |
83 <param name="mode" value="complete" /> | |
84 <param name="out_order" value="ALIGNED" /> | |
85 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> | |
86 <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> | |
87 </test> | |
88 </tests> | |
89 <help> | |
90 | |
91 **Note** | |
92 | |
93 This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options. | |
94 | |
95 For a tutorial introduction, see ClustalW2_ | |
96 | |
97 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file | |
98 | |
99 A log will be output to your history showing the output Clustal would normally write to standard output. | |
100 | |
101 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 | |
102 the output format, you can create a 'Logo' image using the Sequence Logo tool. | |
103 | |
104 If Clustal format is chosen, you have the option of adding basepair counts to the output | |
105 | |
106 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 | |
107 | |
108 ---- | |
109 | |
110 **Attribution** | |
111 | |
112 Clustal attribution and associated documentation are available at Clustsrc_ | |
113 | |
114 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ | |
115 | |
116 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added | |
117 | |
118 This wrapper is released licensed under the LGPL_ | |
119 | |
120 .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html | |
121 | |
122 .. _Clustsrc: http://www.clustal.org | |
123 | |
124 .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html | |
125 | |
126 .. _LGPL: http://www.gnu.org/copyleft/lesser.html | |
127 | |
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128 </help> |
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129 <citations> |
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130 <citation type="doi">10.1093/bioinformatics/btm404</citation> |
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131 </citations> |
0 | 132 </tool> |
133 |