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comparison define_clones.xml @ 6:3ddd933dd7a2 draft default tip

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author davidvanzessen
date Thu, 15 Sep 2016 03:54:33 -0400
parents 326165da9ece
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5:3d97839fda21 6:3ddd933dd7a2
9 </command> 9 </command>
10 <inputs> 10 <inputs>
11 <param name="input" type="data" format="tabular" label="A Change-O DB file" /> 11 <param name="input" type="data" format="tabular" label="A Change-O DB file" />
12 <conditional name="input_type"> 12 <conditional name="input_type">
13 <param name="input_type_select" type="select" label="Input type"> 13 <param name="input_type_select" type="select" label="Input type">
14 <option value="bygroup">Define clones by V assignment, J assignment and junction length</option> 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> 15 <option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option>
16 </param> 16 </param>
17 <when value="bygroup"> 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."> 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> 19 <option value="allele">Allele</option>
20 <option value="gene" selected="true">Gene</option> 20 <option value="gene" selected="true">Gene</option>
21 </param> 21 </param>
22 <param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping."> 22 <param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping.">
23 <option value="first">First</option> 23 <option value="first" selected="true">First</option>
24 <option value="set" selected="true">Set</option> 24 <option value="set">Set</option>
25 </param> 25 </param>
26 <param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences."> 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> 27 <option value="aa">AA hamming distance</option>
28 <option value="ham">Nucleotide 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> 29 <option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option>
30 <option value="hs1f" selected="true">Human single nucleotide (Yaari et al, 2013)</option> 30 <option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option>
31 <option value="hs5f">Human S5F (Yaari et al, 2013)</option> 31 <option value="hs5f">Human S5F (Yaari et al, 2013)</option>
32 </param> 32 </param>
33 <param name="norm" type="select" label="Specifies how to normalize distances."> 33 <param name="norm" type="select" label="Specifies how to normalize distances.">
34 <option value="none">Do not normalize</option> 34 <option value="none" selected="true">Do not normalize</option>
35 <option value="mut">Normalize by number of mutations</option> 35 <option value="mut">Normalize by number of mutations</option>
36 <option value="len" selected="true">Normalize by length</option> 36 <option value="len">Normalize by length</option>
37 </param> 37 </param>
38 <param name="sym" type="select" label="Specifies how to combine asymmetric distances."> 38 <param name="sym" type="select" label="Specifies how to combine asymmetric distances.">
39 <option value="avg" selected="true">Average</option> 39 <option value="avg">Average</option>
40 <option value="min">Minimum</option> 40 <option value="min" selected="true">Minimum</option>
41 </param> 41 </param>
42 <param name="link" type="select" label="Type of linkage to use for hierarchical clustering."> 42 <param name="link" type="select" label="Type of linkage to use for hierarchical clustering.">
43 <option value="single" selected="true">Single</option> 43 <option value="single">Single</option>
44 <option value="average">Average</option> 44 <option value="average">Average</option>
45 <option value="complete">Complete</option> 45 <option value="complete" selected="true">Complete</option>
46 </param> 46 </param>
47 <param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" /> 47 <param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" />
48 </when> 48 </when>
49 <when value="hclust"> 49 <when value="hclust">
50 <param name="method" type="select" label="Specifies which cloning method to use for calculating distance between CDR3s"> 50 <param name="method" type="select" label="Specifies which cloning method to use for calculating distance between CDR3s">