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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_by_metadata" name="filter_by_metadata" version="1.2.0">
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2 <description>Filter OTU table by removal of specified metadata</description>
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3 <requirements>
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4 <requirement type="binary">filter_by_metadata.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='$__new_file_path__'
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9 filter_by_metadata.py
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10 --otu_table_fp=$otu_table_fp
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11 --map=$map
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12 --states=$states
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13 --otu_outfile=$otu_outfile
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14 --map_outfile=$map_outfile
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15 --num_seqs_per_otu=$num_seqs_per_otu
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16 </command>
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17 <inputs>
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18 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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19 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
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20 <param name="map" type="data" format="tabular" label="map"
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21 help="path to the map file [REQUIRED]"/>
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22 <param name="states" type="text" label="states"
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23 help="string containing valid states, e.g. 'STUDY_NAME:DOG' [REQUIRED]"/>
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24 <param name="num_seqs_per_otu" type="integer" value="1" label="num_seqs_per_otu"
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25 help="minimum counts across samples to keep OTU, default is only to keep OTUs that are present in the samples."/>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="otu_outfile"/>
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29 <data format="txt" name="map_outfile"/>
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30 </outputs>
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31 <tests>
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32 </tests>
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33 <help>
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34
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35 </help>
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36 </tool>
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