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