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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="trim_sff_primers" name="trim_sff_primers" version="1.2.0">
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2 <description>Trim sff primers</description>
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3 <requirements>
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4 <requirement type="binary">trim_sff_primers.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='$__new_file_path__'
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9 trim_sff_primers.py
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10 --libdir=$libdir
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11 --input_map=$input_map
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12 --sfffile_path=$sfffile_path
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13 --sffinfo_path=$sffinfo_path
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14 $use_sfftools
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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="libdir" type="text" label="libdir"
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19 help="The directory containing per-library sff files [REQUIRED]"/>
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20 <param name="input_map" type="data" format="tabular" label="input_map"
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21 help="Path to the input mapping file describing the libraries [REQUIRED]"/>
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22 <param name="sfffile_path" type="text" value="sfffile" label="sfffile_path"
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23 help="Path to sfffile binary [default: sfffile]"/>
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24 <param name="sffinfo_path" type="text" value="sffinfo" label="sffinfo_path"
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25 help="Path to sffinfo binary [default: sffinfo]"/>
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26 <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
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27 help="Use external sffinfo and sfffile programs instead of equivalent Python implementation."/>
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28 <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="debug"
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29 help="Print command-line output for debugging [default: False]"/>
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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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