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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="multiple_rarefactions_even_depth" name="multiple_rarefactions_even_depth" version="1.2.0">
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2 <description>Perform multiple rarefactions on a single otu table, at one depth of sequences/sample</description>
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3 <requirements>
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4 <requirement type="binary">multiple_rarefactions_even_depth.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='$__new_file_path__'
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9 multiple_rarefactions_even_depth.py
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10 --input_path=$input_path
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11 --output_path=$output_path
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12 --depth=$depth
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13 --num-reps=$num_reps
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14 $lineages_included
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15 $keep_empty_otus
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16 </command>
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17 <inputs>
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18 <param name="input_path" type="text" label="input_path"
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19 help="input otu table filepath [REQUIRED]"/>
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20 <param name="depth" type="integer" value="-1" label="depth"
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21 help="sequences per sample to subsample [REQUIRED]"/>
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22 <param name="num_reps" type="integer" value="1" label="num-reps"
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23 help="num iterations at each seqs/sample level [default: 1]"/>
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24 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
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25 help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
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26 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
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27 help="otus (rows) of all zeros are usually omitted from the output otu tables, with -k they will not be removed from the output files [default: False]"/>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="output_path"/>
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31 </outputs>
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32 <tests>
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33 </tests>
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34 <help>
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35
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36 </help>
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37 </tool>
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