Mercurial > repos > davidvanzessen > change_o
comparison define_clones.xml @ 0:183edf446dcf draft default tip
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author | davidvanzessen |
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date | Mon, 17 Jul 2017 07:44:27 -0400 |
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-1:000000000000 | 0:183edf446dcf |
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1 <tool id="change_o_define_clones_galaxy" name="Define Clones" version="1.0"> | |
2 <description>Change-O</description> | |
3 <command interpreter="bash"> | |
4 #if $input_type.input_type_select=="bygroup" | |
5 define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file $out_file2 | |
6 #else | |
7 define_clones.sh hclust $input $input_type.method $out_file $out_file2 | |
8 #end if | |
9 </command> | |
10 <inputs> | |
11 <param name="input" type="data" format="tabular" label="A Change-O DB file" /> | |
12 <conditional name="input_type"> | |
13 <param name="input_type_select" type="select" label="Input type"> | |
14 <option value="bygroup" selected="true">Define clones by V assignment, J assignment and junction length</option> | |
15 <option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option> | |
16 </param> | |
17 <when value="bygroup"> | |
18 <param name="mode" type="select" label="Specifies whether to use the V(D)J allele or gene for initial grouping."> | |
19 <option value="allele">Allele</option> | |
20 <option value="gene" selected="true">Gene</option> | |
21 </param> | |
22 <param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping."> | |
23 <option value="first" selected="true">First</option> | |
24 <option value="set">Set</option> | |
25 </param> | |
26 <param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences."> | |
27 <option value="aa">AA hamming distance</option> | |
28 <option value="ham" selected="true">Nucleotide hamming distance</option> | |
29 <option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option> | |
30 <option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option> | |
31 <option value="hs5f">Human S5F (Yaari et al, 2013)</option> | |
32 </param> | |
33 <param name="norm" type="select" label="Specifies how to normalize distances."> | |
34 <option value="none" selected="true">Do not normalize</option> | |
35 <option value="mut">Normalize by number of mutations</option> | |
36 <option value="len">Normalize by length</option> | |
37 </param> | |
38 <param name="sym" type="select" label="Specifies how to combine asymmetric distances."> | |
39 <option value="avg">Average</option> | |
40 <option value="min" selected="true">Minimum</option> | |
41 </param> | |
42 <param name="link" type="select" label="Type of linkage to use for hierarchical clustering."> | |
43 <option value="single">Single</option> | |
44 <option value="average">Average</option> | |
45 <option value="complete" selected="true">Complete</option> | |
46 </param> | |
47 <param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" /> | |
48 </when> | |
49 <when value="hclust"> | |
50 <param name="method" type="select" label="Specifies which cloning method to use for calculating distance between CDR3s"> | |
51 <option value="chen2010" selected="true">Chen et al 2010</option> | |
52 <option value="ademokun2011">Ademokun et al 2011</option> | |
53 </param> | |
54 </when> | |
55 </conditional> | |
56 </inputs> | |
57 <outputs> | |
58 <data format="tabular" name="out_file" label = "Change-o DB clones ${input.name}"/> | |
59 <data format="tabular" name="out_file2" label = "Change-o DB clones info ${input.name}"/> | |
60 </outputs> | |
61 <citations> | |
62 <citation type="doi">10.1093/bioinformatics/btv359</citation> | |
63 </citations> | |
64 <help> | |
65 | |
66 | |
67 </help> | |
68 </tool> |