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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="process_sff" name="process_sff" version="1.2.0">
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2 <description>Convert sff to FASTA and QUAL files</description>
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3 <requirements>
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4 <requirement type="binary">process_sff.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='$__new_file_path__'
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9 process_sff.py
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10 --input_dir=$input_dir
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11 $make_flowgram
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12 $convert_to_FLX
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13 $use_sfftools
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14 --output_dir=$__new_file_path__
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15 </command>
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16 <inputs>
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17 <param name="input_dir" type="text" label="input_dir"
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18 help="Input directory of sff files [REQUIRED]"/>
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19 <param name="make_flowgram" type="boolean" truevalue="--make_flowgram" falsevalue="" checked="false" label="make_flowgram"
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20 help="generate a flowgram file. [default: False]"/>
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21 <param name="convert_to_FLX" type="boolean" truevalue="--convert_to_FLX" falsevalue="" checked="false" label="convert_to_FLX"
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22 help="convert Titanium reads to FLX length. [default: False]"/>
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23 <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
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24 help="use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation"/>
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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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35