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comparison define_clones.xml @ 0:183edf446dcf draft default tip

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author davidvanzessen
date Mon, 17 Jul 2017 07:44:27 -0400
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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>