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annotate make_otu_table.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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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_make_otu_table" name="make otu table" version="1.9.1galaxy1">
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3 <description>Make OTU table</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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8
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9 <expand macro="requirements" />
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10
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11 <command>
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12 <![CDATA[
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13 make_otu_table.py
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14 -i $otu_map_fp
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15 -o $output_biom_fp
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16 #if str($taxonomy) != 'None':
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17 -t $taxonomy
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18 #end if
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19
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20 #if str($exclude_otus_fp) != 'None':
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21 -e $exclude_otus_fp
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22 #end if
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27 <param label="-i/--otu_map_fp: path to the input OTU map (i.e., the output
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28 from pick_otus.py)" name="otu_map_fp" optional="False" type="data"/>
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29 <param label="-t/--taxonomy: Path to taxonomy assignment, containing the
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30 assignments of taxons to sequences (i.e., resulting txt file from
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31 assign_taxonomy.py) [default: None]" name="taxonomy" optional="True"
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32 type="data"/>
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33 <param label="-e/--exclude_otus_fp: path to a file listing OTU identifiers
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34 that should not be included in the OTU table (e.g., the output of
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35 identify_chimeric_seqs.py) or a fasta file where seq ids should be
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36 excluded (e.g., failures fasta file from align_seqs.py)"
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37 name="exclude_otus_fp" optional="True" type="data"/>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="txt" name="output_biom_fp" label="otu_table.biom"/>
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 </test>
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47 </tests>
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48
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49 <help><![CDATA[
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50
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51 **What it does**
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52
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53 The script make_otu_table.py tabulates the number of times an OTU is found in each
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54 sample, and adds the taxonomic predictions for each OTU in the last column if a
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55 taxonomy file is supplied.
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56 The output of make_otu_table.py is a biom file, where the columns correspond to
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57 Samples and rows correspond to OTUs and the number of times a sample appears in
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58 a particular OTU.
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59 ]]>
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60 </help>
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61
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62 <citations>
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63 <expand macro="citations" />
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64 </citations>
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65 </tool>