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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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1 <tool id="otu_category_significance" name="otu_category_significance" version="1.2.0">
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2 <description>OTU significance and co-occurence analysis</description>
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3 <requirements>
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4 <requirement type="binary">otu_category_significance.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 --galaxy_tmpdir='$__new_file_path__'
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9 otu_category_significance.py
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10 --otu_table_fp=$otu_table_fp
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11 --category_mapping_fp=$category_mapping_fp
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12 --category=$category
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13 --test=$test
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14 --output_fp=$output_fp
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15 --filter=$filter
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16 --threshold=$threshold
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17 --otu_include_fp=$otu_include_fp
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18 </command>
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19 <inputs>
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20 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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21 help="path to the otu table, or to a directory containing OTU tables [REQUIRED]"/>
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22 <param name="category_mapping_fp" type="data" format="tabular" label="category_mapping_fp"
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23 help="path to category mapping file [REQUIRED]"/>
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24 <param name="category" type="text" label="category"
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25 help="name of category over which to run the analysis [REQUIRED]"/>
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26 <param name="test" type="text" value="g_test" label="test"
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27 help="the type of statistical test to run. options are: g_test: determines whether OTU presence/absence is associated with a category using the G test of independence. ANOVA: determines whether OTU abundance is associated with a category. correlation: determines whether OTU abundance is correlated with a continuous variable in the category mapping file."/>
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28 <param name="filter" type="text" value="10" label="filter"
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29 help="minimum number of samples that must contain the OTU for the OTU to be included in the analysis. default value=10."/>
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30 <param name="threshold" type="text" label="threshold"
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31 help="threshold under which to consider something absent: Only used if you have numerical data that should be converted to present or absent based on a threshold. Should be None for categorical data or with the correlation test. default value is None"/>
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32 <param name="otu_include_fp" type="data" format="txt" label="otu_include_fp"
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33 help="path to a file with a list of OTUs to evaluate. By default evaluates all OTUs that pass the minimum sample filter. If a filepath is given here in which each OTU name one wishes to evaluate is on a separate line, will apply this additional filter"/>
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34 </inputs>
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35 <outputs>
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36 <data format="txt" name="output_fp"/>
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37 </outputs>
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38 <tests>
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39 </tests>
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40 <help>
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41
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42 </help>
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43 </tool>
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