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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author iuc
date Fri, 23 Apr 2021 03:04:15 +0000
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children 112d80c9ccca
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af03f3398f03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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1 <tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@">
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2 <description>sequences that lie within a specific distance of each other</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">tn93</requirement>
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8 <requirement type="package" version="3.9">python</requirement>
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9 </requirements>
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10 <version_command><![CDATA[tn93 --version]]></version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
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13 --threshold $threshold
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14 --ambigs $ambigs
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15 --cluster-type $cluster_type
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16 --overlap $overlap
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17 --fraction $fraction
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18 --cluster-count $cluster_count
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19 #if $compress:
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20 --compressed '$tn93_compressed_clusters'
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
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25 <param name="reference" type="data" format="fasta" label="Reference in FASTA format" />
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26 <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" />
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27 <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" />
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28 <param argument="--threshold" type="float" min="0" value="0.0005" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
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29 <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
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30 <option value="resolve" selected="true">resolve</option>
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31 <option value="average">average</option>
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32 <option value="skip">skip</option>
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33 <option value="gapmm">gapmm</option>
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34 </param>
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35 <param argument="--cluster_type" type="select" label="Clustering rules" help="&quot;All&quot;: Each sequence within the cluster must be within the specified distance of every other sequence in the cluster. &quot;Any&quot;: Each sequence within the cluster must be within the specified distance of at least one other sequence.">
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36 <option value="all">All</option>
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37 <option value="any">Any</option>
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38 </param>
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39 <param name="overlap" argument="-l" type="integer" value="100"
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40 label="Only process pairs that overlap by at least N bases" />
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41 <param name="fraction" argument="-g" type="float" value="1.0"
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42 label="Maximum tolerated fraction of ambiguous characters" />
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43 </inputs>
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44 <outputs>
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45 <data format="json" name="tn93_clusters" />
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46 <data format="fasta" name="tn93_compressed_clusters">
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47 <filter>compress</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="2">
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52 <param name="input_fasta" value="cluster-in1-1.fa" />
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53 <param name="reference" value="cluster-in1-2.fa" />
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54 <param name="threshold" value="0.35" />
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55 <param name="compress" value="true" />
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56 <output file="cluster-out1.json" ftype="json" name="tn93_clusters" />
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57 <output file="cluster-out1.fa" ftype="fasta" name="tn93_compressed_clusters" />
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 TN93-Cluster
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62 ============
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63
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64 Clusters sequences within a minimum distance of each other using the 1993
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65 Tamura-Nei distance calculation.
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66
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67 ]]></help>
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68 <expand macro="citations">
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69 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
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70 </expand>
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71 </tool>