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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="shared_phylotypes" name="shared_phylotypes" version="1.2.0">
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2 <description>Compute shared OTUs between all pairs of samples</description>
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3 <requirements>
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4 <requirement type="binary">shared_phylotypes.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='$__new_file_path__'
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9 shared_phylotypes.py
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10 --otu_table_fp=$otu_table_fp
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11 --output_fp=$output_fp
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12 --reference_sample=$reference_sample
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13 $force_overwrite
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14 </command>
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15 <inputs>
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16 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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17 help="path to the input OTU table or a directory containing (only) OTU tables [REQUIRED]"/>
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18 <param name="reference_sample" type="text" label="reference_sample"
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19 help="Name of reference sample to which all pairs of samples should be compared [default: %default]"/>
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20 <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
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21 help="Overwrite output_fp if already exists [default: ('NO', 'DEFAULT')]"/>
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22 </inputs>
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23 <outputs>
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24 <data format="txt" name="output_fp"/>
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help>
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29
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30 </help>
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31 </tool>
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