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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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1 <tool id="shared_phylotypes" name="shared_phylotypes" version="1.2.0">
2 <description>Compute shared OTUs between all pairs of samples</description>
3 <requirements>
4 <requirement type="binary">shared_phylotypes.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 shared_phylotypes.py
10 --otu_table_fp=$otu_table_fp
11 --output_fp=$output_fp
12 --reference_sample=$reference_sample
13 $force_overwrite
14 </command>
15 <inputs>
16 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
17 help="path to the input OTU table or a directory containing (only) OTU tables [REQUIRED]"/>
18 <param name="reference_sample" type="text" label="reference_sample"
19 help="Name of reference sample to which all pairs of samples should be compared [default: %default]"/>
20 <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
21 help="Overwrite output_fp if already exists [default: ('NO', 'DEFAULT')]"/>
22 </inputs>
23 <outputs>
24 <data format="txt" name="output_fp"/>
25 </outputs>
26 <tests>
27 </tests>
28 <help>
29
30 </help>
31 </tool>
32