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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="summarize_taxa" name="summarize_taxa" version="1.2.1">
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2 <description>Summarize Taxa</description>
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3 <requirements>
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4 <requirement type="binary">summarize_taxa.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 summarize_taxa.py
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9 --otu_table_fp=$otu_table_fp
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10 --output_fp=$output_fp
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11 --level=$level
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12 #if $mapping != None and $mapping.__str__ != 'None':
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13 --mapping=$mapping
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14 #end if
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15 #if $delimiter != ';':
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16 --delimiter=$delimiter
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17 #end if
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18 ## --relative_abundance=$relative_abundance
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19 $absolute_abundance
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20 </command>
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21 <inputs>
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22 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
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23 help="Path to read otu file [REQUIRED]"/>
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24 <param name="level" type="integer" value="2" label="level"
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25 help="Level of taxonomy to use [default: 2]"/>
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26 <param name="mapping" type="data" format="qiimemapping" optional="true" label="mapping"
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27 help="if supplied - the taxon information will be added to the mapping file. This mapping file can be used to color PCoA plots by taxon abundance or to perform statistical tests of taxon/mappingy associations."/>
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28 <param name="delimiter" type="text" value="\;" label="delimiter"
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29 help="Delimitor that separates taxonomy categories.[default: ;]"/>
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30 <param name="absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="absolute_abundance"
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31 help="If present, reports the absolute abundance of the lineage in each sample. By default uses relative abundance [default: False]"/>
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32 </inputs>
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33 <outputs>
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34 <data format="qiimetaxsummary" name="output_fp" label="${tool.name} on ${on_string}: taxa_summary"/>
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35 </outputs>
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36 <tests>
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37 </tests>
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38 <help>
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39
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40 </help>
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41 </tool>
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