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annotate make_phylogeny.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_make_phylogeny" name="Make phylogeny" version="1.9.1">
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3 <description></description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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9 <expand macro="requirements" />
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11 <version_command><![CDATA[
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12 make_phylogeny.py --version
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13 ]]>
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14 </version_command>
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16 <stdio></stdio>
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18 <command>
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19 <![CDATA[
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20 make_phylogeny.py
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21 -i $input_fp
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22 -o $result_fp
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23 -t $tree_method
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24 -l $log_fp
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25 -r $root_method
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26 ]]>
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27 </command>
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29 <inputs>
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30 <param name="input_fp" type="data" format="fasta"
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31 label="Input fasta alignment" help="(-i/--input_fp)"/>
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32
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33 <param name="tree_method" type="select"
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34 label="Method for tree building" help="(-t/--tree_method)">
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35 <option value="clustalw">ClustalW</option>
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36 <option value="raxml_v730">raxml_v730</option>
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37 <option value="muscle">muscle</option>
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38 <option value="fasttree" selected="true">fasttree</option>
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39 <option value="clearcut">clearcut</option>
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40 </param>
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41
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42 <param name="root_method" type="select"
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43 label="Method for choosing root of phylo tree" help="(-r/--root_method)">
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44 <option value="midpoint">Midpoint</option>
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45 <option value="tree_method_default" selected="true">Default method of tree method</option>
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46 </param>
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47
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48 </inputs>
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49
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50 <outputs>
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51 <data format="txt" name="result_fp"
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52 label="${tool.name} on ${on_string}: Tree"/>
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53 <data format="txt" name="log_fp"
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54 label="${tool.name} on ${on_string}: Log"/>
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 </test>
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60 </tests>
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61
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62 <help><![CDATA[
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63 **What it does**
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64
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65 This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
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66
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67 More information about this tool is available on
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68 `QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
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69 ]]>
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70 </help>
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71
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72 <citations>
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73 <expand macro="citations" />
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74 </citations>
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75 </tool>