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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="make_library_id_lists" name="make_library_id_lists" version="1.2.0">
2 <description>Make library id lists</description>
3 <requirements>
4 <requirement type="binary">make_library_id_lists.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 make_library_id_lists.py
10 --input_fasta=$input_fasta
11 --screened_rep_seqs=$screened_rep_seqs
12 --otus=$otus
13 --outdir=$outdir
14 --field=$field
15 $debug
16 </command>
17 <inputs>
18 <param name="input_fasta" type="data" format="fasta" label="input_fasta"
19 help="The path to a FASTA file containing input sequences [REQUIRED]"/>
20 <param name="screened_rep_seqs" type="text" label="screened_rep_seqs"
21 help="The path to a FASTA file containing screened representative seqs[DEFAULT: %default]"/>
22 <param name="otus" type="text" label="otus"
23 help="The path to an OTU file mapping OTUs onto rep seqs[DEFAULT: %default]"/>
24 <param name="outdir" type="text" value="." label="outdir"
25 help=" The base directory to save results (one file per library)."/>
26 <param name="field" type="integer" value="1" label="field"
27 help="Index of space-delimited field to read id from [DEFAULT: 1]"/>
28 <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="debug"
29 help="Show debug output."/>
30 </inputs>
31 <outputs>
32
33 </outputs>
34 <tests>
35 </tests>
36 <help>
37
38 </help>
39 </tool>
40