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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="make_otu_table" name="make_otu_table" version="1.2.0">
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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=$otu_map_fp
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10 --taxonomy=$taxonomy
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11 --exclude_otus_fp=$exclude_otus_fp
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12 --output_fp=$output_fp
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13 </command>
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14 <inputs>
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15 <param name="otu_map_fp" type="data" format="qiimeotu" label="otu_map_fp"
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16 help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
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17 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy"
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18 help="Path to taxonomy assignment, containing the assignments of \ taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [default: %default]"/>
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19 <param name="exclude_otus_fp" type="data" format="txt" label="exclude_otus_fp"
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20 help="a filepath listing OTU identifiers that should not be included in the OTU table (e.g., the output of identify_chimeric_seqs.py)"/>
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21 </inputs>
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22 <outputs>
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23 <data format="qiimeotutable" name="output_fp" label="${tool.name} on ${on_string}: otu_table"/>
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24 </outputs>
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25 <tests>
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26 </tests>
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27 <help>
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28
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29 </help>
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30 </tool>
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