Mercurial > repos > xuebing > kplogo
comparison kplogo.xml @ 1:3c13235a05f5 draft
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author | xuebing |
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date | Fri, 24 Mar 2017 16:09:26 -0400 |
parents | f6226f8823ce |
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0:f6226f8823ce | 1:3c13235a05f5 |
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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 |