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1 <tool id="cluster-pick" name="Cluster Picker" version="1.2.3">
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2 <description>cluster picker</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.3">cluster-picker</requirement>
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5 </requirements>
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6 <command> <![CDATA[ln -s '$sequence_file' seq.dat &&
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7 ln -s '$tree_file' tree.dat &&
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8 cluster-picker seq.dat tree.dat $init_threshold $main_threshold $dis_threshold $size $genetic_distance
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9 ]]> </command>
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10 <inputs>
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11 <param format="fasta" name="sequence_file" type="data" label="align"
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12 help="Please enter fasta format sequences file name to process"/>
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13 <param format="nhx" name="tree_file" type="data" label="tree"
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14 help="Please enter newick format tree, with branch lengths and node support"/>
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15 <param name="init_threshold" type="float" value="0.9" optional="true"
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16 help="Please enter initial support threshold for these initial subtrees" label="initial threshold">
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17 </param>
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18 <param name="main_threshold" type="float" value="0.9" optional="true"
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19 help="Please enter main support threshold for clusters" label="main threshold">
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20 </param>
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21 <param name="dis_threshold" type="float" value="0.045" optional="true"
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22 help="Please enter genetic distance threshold for clusters in %" label="distance threshold">
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23 </param>
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24 <param name="size" type="integer" value="10" optional="true"
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25 help="To output all cluster names for clusters of size >= X enter X" label="size">
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26 </param>
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27 <param name="genetic_distance" type="select" label="genetic distance"
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28 help="Please enter scoring type for genetic distance\n
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29 gap = disregard sites with -, ~, or n\n
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30 abs = count absolute character differences\n
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31 valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n
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32 ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)">
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33 <option value="gap">gap</option>
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34 <option value="abs">abs</option>
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35 <option value="valid">valid</option>
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36 <option value="ambiguity">ambiguity</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data name='fig' format="figTree" from_work_dir="tree_clusterPicks.nwk.figTree"/>
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41 <data name='tr' format="nhx" from_work_dir="tree_clusterPicks.nwk"/>
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42 <data name='log' format="txt" from_work_dir="tree_clusterPicks_log.txt"/>
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43 <data name='seq' format="fasta" from_work_dir="seq.dat_tree_clusterPicks.fasta"/>
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="sequence_file" value="dummy.fasta" />
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49 <param name="tree_file" value="dummy.nhx" />
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50 <param name="init_threshold" value="0.9" />
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51 <param name="main_threshold" value="0.9" />
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52 <param name="dis_threshold" value="0.045" />
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53 <param name="size" value="10" />
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54 <param name="genetic_distance" value="gap" />
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55 <param name="main_threshold" file="0.9" />
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56 <output name="fig" file="dummy.figTree" />
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57 </test>
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58 </tests>
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59
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60 <help>
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61 Cluster identification strategies differ between studies and as a consequence cluster definitions vary.
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62 </help>
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63 <citations>
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64 <citation type="bibtex">@ARTICLE{cluster-picker,
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65 author = {Ragonnet-Cronin, Manon, et al;},
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66 title = {Automated analysis of phylogenetic clusters},
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67 journal = {BMC bioinformatics},
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68 year = {2013},
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69 volume = {14.1},
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70 pages = {317}}
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71 </citation>
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72 </citations>
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73 </tool>
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