Mercurial > repos > jjohnson > qiime
comparison otu_category_significance.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="otu_category_significance" name="otu_category_significance" version="1.2.0"> | |
| 2 <description>OTU significance and co-occurence analysis</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">otu_category_significance.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 otu_category_significance.py | |
| 10 --otu_table_fp=$otu_table_fp | |
| 11 --category_mapping_fp=$category_mapping_fp | |
| 12 --category=$category | |
| 13 --test=$test | |
| 14 --output_fp=$output_fp | |
| 15 --filter=$filter | |
| 16 --threshold=$threshold | |
| 17 --otu_include_fp=$otu_include_fp | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp" | |
| 21 help="path to the otu table, or to a directory containing OTU tables [REQUIRED]"/> | |
| 22 <param name="category_mapping_fp" type="data" format="tabular" label="category_mapping_fp" | |
| 23 help="path to category mapping file [REQUIRED]"/> | |
| 24 <param name="category" type="text" label="category" | |
| 25 help="name of category over which to run the analysis [REQUIRED]"/> | |
| 26 <param name="test" type="text" value="g_test" label="test" | |
| 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."/> | |
| 28 <param name="filter" type="text" value="10" label="filter" | |
| 29 help="minimum number of samples that must contain the OTU for the OTU to be included in the analysis. default value=10."/> | |
| 30 <param name="threshold" type="text" label="threshold" | |
| 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"/> | |
| 32 <param name="otu_include_fp" type="data" format="txt" label="otu_include_fp" | |
| 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"/> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="txt" name="output_fp"/> | |
| 37 </outputs> | |
| 38 <tests> | |
| 39 </tests> | |
| 40 <help> | |
| 41 | |
| 42 </help> | |
| 43 </tool> | |
| 44 |