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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="merge_denoiser_output" name="merge_denoiser_output" version="1.2.0">
2 <description>Merge the output of denoising step back into QIIME</description>
3 <requirements>
4 <requirement type="binary">merge_denoiser_output.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 merge_denoiser_output.py
10 --map_file=$map_file
11 --otu_picker_map_file=$otu_picker_map_file
12 --fasta_fp=$fasta_fp
13 --denoised_fasta_fp=$denoised_fasta_fp
14 --output_dir=$__new_file_path__
15 </command>
16 <inputs>
17 <param name="map_file" type="data" format="tabular" label="map_file"
18 help="path to denoiser cluster mapping file [REQUIRED]"/>
19 <param name="otu_picker_map_file" type="data" format="tabular" label="otu_picker_map_file"
20 help="path to OTU mapping file from OTU picker [REQUIRED]"/>
21 <param name="fasta_fp" type="data" format="fasta" label="fasta_fp"
22 help="path to FASTA file, output of split_libraries.py [REQUIRED]"/>
23 <param name="denoised_fasta_fp" type="data" format="fasta" label="denoised_fasta_fp"
24 help="path to denoised fasta file [REQUIRED]"/>
25 </inputs>
26 <outputs>
27
28 </outputs>
29 <tests>
30 </tests>
31 <help>
32
33 </help>
34 </tool>
35