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