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1 <tool id="make_otu_table" name="make_otu_table" version="2.0.0">
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2 <description>Make OTU table</description>
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3 <requirements>
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4 <requirement type="binary">make_otu_table.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 make_otu_table.py
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9 --otu_map_fp=$otu_map_fp
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10 --output_fp=$output_fp
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11 #if $taxonomy.__str__ != 'None':
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12 --taxonomy=$taxonomy
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13 #end if
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14 #if $exclude_otus_fp.__str__ != 'None':
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15 --exclude_otus_fp=$exclude_otus_fp
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16 #end if
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17 </command>
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18 <inputs>
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19 <param name="otu_map_fp" type="data" format="qiimeotu" label="otu_map_fp"
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20 help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
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21 <param name="taxonomy" type="data" format="seq.taxonomy" optional="true" label="taxonomy"
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22 help="Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [OPTIONAL]"/>
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23 <param name="exclude_otus_fp" type="data" format="txt" optional="true" label="exclude_otus_fp"
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24 help="a filepath listing OTU identifiers that should not be included in the OTU table (e.g., the output of identify_chimeric_seqs.py) or a fasta file where seq ids should be excluded (e.g., failures fasta file from align_seqs.py) [OPTIONAL]"/>
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25 </inputs>
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26 <outputs>
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27 <data format="qiimeotutable" name="output_fp" label="${tool.name} on ${on_string}: otu_table"/>
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28 </outputs>
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29 <tests>
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30 </tests>
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31 <help>For more information, see make_otu_table_ in the Qiime documentation.
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32
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33 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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34
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35 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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36
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37 .. _make_otu_table: http://qiime.org/scripts/make_otu_table</help>
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38 </tool>
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39
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