Mercurial > repos > xuebing > kplogo

comparison kplogo.xml @ 1:3c13235a05f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 24 Mar 2017 16:09:26 -0400
parents f6226f8823ce
children
comparison
equal deleted inserted replaced
0:f6226f8823ce 1:3c13235a05f5
1 <tool id="kplogo" name="kpLogo" version="1.0"> 1 <tool id="kplogo" name="kpLogo" version="1.0">
2 <description>for positional k-mer analysis</description> 2 <description>for positional k-mer analysis</description>
3 <command> 3 <command>
4 4
5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate 2> tmp; 5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end 2> tmp;
6 cp ${output}.most.significant.each.position.pdf $output; 6 cp ${output}.most.significant.each.position.pdf $output;
7 cp ${output}.pdf $logo_prob; 7 cp ${output}.pdf $logo_prob;
8 cp ${output}.info.pdf $logo_info; 8 cp ${output}.info.pdf $logo_info;
9 cp ${output}.freq.pdf $logo_freq; 9 cp ${output}.freq.pdf $logo_freq;
10 cp ${output}.most.significant.each.position.txt $tab_most; 10 cp ${output}.most.significant.each.position.txt $tab_most;
11 cp ${output}.pass.p.cutoff.txt $tab_all; 11 cp ${output}.pass.p.cutoff.txt $tab_all;
12 12
13 </command> 13 </command>
14 <inputs> 14 <inputs>
15 <page> 15 <page>
16 <param format="fasta" name="input" type="data" label="Fasta File" /> 16 <param format="text" name="input" type="data" label="Input sequences (FASTA or Tabular)" />
17 17
18 <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" > 18 <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
19 <option value="dna" selected="True">DNA/RNA</option> 19 <option value="dna" selected="True">DNA/RNA</option>
20 <option value="protein">Protein</option> 20 <option value="protein">Protein</option>
21 <option value="other">Other (not supported yet)</option> 21 <option value="other">Other (not supported yet)</option>
22 </param> 22 </param>
24 <param name="inputtype" type="select" label="Weighted or Ranked" > 24 <param name="inputtype" type="select" label="Weighted or Ranked" >
25 <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option> 25 <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
26 <option value="-ranked">Ranked (FASTA or Tab-delimited)</option> 26 <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
27 <option value="-weighted">Weighted (Tab-delimited)</option> 27 <option value="-weighted">Weighted (Tab-delimited)</option>
28 </param> 28 </param>
29
30
31 <param name="col_seq" type="integer" value="1" label="For tabular input, sequence is in this column:" />
32
33 <param name="col_weight" type="integer" value="2" label="For tabular input, weight is in this column:" />
34
35 <param name="region_start" type="integer" value="1" label="Starting from position (0 or negative numbers interpreted as distance from the end):" />
36
37 <param name="region_end" type="integer" value="0" label="Ending at position (0 or negative numbers interpreted as distance from the end):" />
38
39
29 40
30 <param name="maxk" type="select" label="k-mer length" 41 <param name="maxk" type="select" label="k-mer length"
31 help="k-mer length"> 42 help="k-mer length">
32 <option value="-max_k 4" selected="True">1,2,3,4</option> 43 <option value="-max_k 4" selected="True">1,2,3,4</option>
33 <option value="-max_k 3">1,2,3</option> 44 <option value="-max_k 3">1,2,3</option>
42 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option> 53 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
43 <option value="">None (no degenerate residuals)</option> 54 <option value="">None (no degenerate residuals)</option>
44 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option> 55 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
45 </param> 56 </param>
46 57
47 <param name="startPos" type="integer" value="1"/> 58 <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." />
48 59
60 <param name="fix" type="float" value="0.75" label="Fixation frequency"/>
49 61
50 </page> 62 </page>
51 </inputs> 63 </inputs>
52 <outputs> 64 <outputs>
53 <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/> 65 <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/>
61 </outputs> 73 </outputs>
62 <help> 74 <help>
63 75
64 **Note** 76 **Note**
65 77
66 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. 78 This is a wrapper for the positional k-mer analysis tool kpLogo_, which is also available as a web server and stand-alone command-line tool. Please refer to the manual_ on the web server for help information.
67 79
68 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed 80 To run kpLogo on local Galaxy instances, one needs to compile and install kpLogo locally. Please refer to the web server for details (click here_).
69 it in to this tool.
70
71 A typical output looks like this
72
73 .. image:: ${static_path}/images/rgWebLogo3_test.jpg
74 81
75 ---- 82 ----
76 83
77 **Warning about input Fasta format files**
78 84
79 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning 85 .. _kpLogo: http://kplogo.wi.mit.edu/
80 and refuse to call the weblogo3 executable if irregular length sequences are detected.
81 86
82 Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file 87 .. _manual: http://kplogo.wi.mit.edu/manual.html
83 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta 88
84 sequences are the same length! 89 .. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally
85 90
86 ----
87
88 **Attribution**
89
90 Weblogo attribution and associated documentation are available at Weblogo3_
91
92 This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
93
94 .. _Weblogo3: http://weblogo.berkeley.edu/
95
96 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
97 91
98 </help> 92 </help>
99 93
100 </tool> 94 </tool>
101 95