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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="filter_otu_table" name="filter_otu_table" version="1.2.0">
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2 <description>Filters OTU table by minimum OTU count and number of samples or by taxonomy</description>
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3 <requirements>
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4 <requirement type="binary">filter_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 --galaxy_tmpdir='$__new_file_path__'
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9 filter_otu_table.py
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10 --otu_table_fp=$otu_table_fp
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11 --min_count=$min_count
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12 --min_samples=$min_samples
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13 --include_taxonomy=$include_taxonomy
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14 --exclude_taxonomy=$exclude_taxonomy
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15 --dir_path=$dir_path
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16 --seqs_per_sample=$seqs_per_sample
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17 </command>
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18 <inputs>
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19 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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20 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
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21 <param name="min_count" type="integer" value="1" label="min_count"
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22 help="retain OTUs with at least this many sequences [default=1]"/>
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23 <param name="min_samples" type="integer" value="2" label="min_samples"
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24 help="retain OTUs found in at least this many samples [default=2]"/>
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25 <param name="include_taxonomy" type="text" value="" label="include_taxonomy"
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26 help="list of taxonomy terms to include [default=]"/>
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27 <param name="exclude_taxonomy" type="text" value="" label="exclude_taxonomy"
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28 help="list of taxonomy terms to exclude [default=]"/>
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29 <param name="dir_path" type="text" value="./" label="dir_path"
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30 help="directory prefix for all analyses [default=./]"/>
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31 <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
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32 help="minimum sequences per sample to retain the sample. [default=('NO', 'DEFAULT')]"/>
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33 </inputs>
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34 <outputs>
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35
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help>
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40
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41 </help>
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42 </tool>
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43