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