Mercurial > repos > xuebing > kplogo
comparison kplogo.xml @ 3:7c3170671f1b draft
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author | xuebing |
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date | Fri, 24 Mar 2017 16:09:56 -0400 |
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children | 00b951fec5f7 |
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2:aa036496c27a | 3:7c3170671f1b |
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1 <tool id="kplogo" name="kpLogo" version="1.0"> | |
2 <description>for positional k-mer analysis</description> | |
3 <command> | |
4 | |
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; | |
7 cp ${output}.pdf $logo_prob; | |
8 cp ${output}.info.pdf $logo_info; | |
9 cp ${output}.freq.pdf $logo_freq; | |
10 cp ${output}.most.significant.each.position.txt $tab_most; | |
11 cp ${output}.pass.p.cutoff.txt $tab_all; | |
12 | |
13 </command> | |
14 <inputs> | |
15 <page> | |
16 <param format="text" name="input" type="data" label="Input sequences (FASTA or Tabular)" /> | |
17 | |
18 <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" > | |
19 <option value="dna" selected="True">DNA/RNA</option> | |
20 <option value="protein">Protein</option> | |
21 <option value="other">Other (not supported yet)</option> | |
22 </param> | |
23 | |
24 <param name="inputtype" type="select" label="Weighted or Ranked" > | |
25 <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option> | |
26 <option value="-ranked">Ranked (FASTA or Tab-delimited)</option> | |
27 <option value="-weighted">Weighted (Tab-delimited)</option> | |
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 | |
40 | |
41 <param name="maxk" type="select" label="k-mer length" | |
42 help="k-mer length"> | |
43 <option value="-max_k 4" selected="True">1,2,3,4</option> | |
44 <option value="-max_k 3">1,2,3</option> | |
45 <option value="-max_k 2">1,2</option> | |
46 <option value="-k 4">4</option> | |
47 <option value="-k 3">3</option> | |
48 <option value="-k 2">2</option> | |
49 <option value="-k 1">1</option> | |
50 </param> | |
51 | |
52 <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)"> | |
53 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option> | |
54 <option value="">None (no degenerate residuals)</option> | |
55 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option> | |
56 </param> | |
57 | |
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)." /> | |
59 | |
60 <param name="fix" type="float" value="0.75" label="Fixation frequency"/> | |
61 | |
62 </page> | |
63 </inputs> | |
64 <outputs> | |
65 <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/> | |
66 <data format="pdf" name="logo_freq" label="${tool.name} on ${on_string}: freq"/> | |
67 <data format="pdf" name="logo_prob" label="${tool.name} on ${on_string}: prob"/> | |
68 <data format="pdf" name="output" label="${tool.name} on ${on_string}: kmer"/> | |
69 <data format="tabular" name="tab_all" label="${tool.name} on ${on_string}: all_kmer"/> | |
70 <data format="tabular" name="tab_most" label="${tool.name} on ${on_string}: most_sig"/> | |
71 | |
72 | |
73 </outputs> | |
74 <help> | |
75 | |
76 **Note** | |
77 | |
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. | |
79 | |
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_). | |
81 | |
82 ---- | |
83 | |
84 | |
85 .. _kpLogo: http://kplogo.wi.mit.edu/ | |
86 | |
87 .. _manual: http://kplogo.wi.mit.edu/manual.html | |
88 | |
89 .. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally | |
90 | |
91 | |
92 </help> | |
93 | |
94 </tool> | |
95 | |
96 |