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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="check_id_map" name="check_id_map" version="1.2.0">
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2 <description>Checks user's metadata mapping file for required data, valid format</description>
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3 <requirements>
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4 <requirement type="binary">check_id_map.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_outputdir='$log.extra_files_path'
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9 --galaxy_datasets='^\S+_corrected\.txt$:'$corrected_mapping,'^\S+\.log:'$log
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10 check_id_map.py
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11 --map=$map
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12 --output_dir='$log.extra_files_path'
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13 --char_replace=$char_replace
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14 $not_barcoded
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15 $variable_len_barcodes
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16 $disable_primer_check
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17 $verbose
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18 </command>
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19 <inputs>
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20 <param name="map" type="data" format="tabular" label="map"
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21 help="Metadata mapping file filepath [REQUIRED]"/>
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22 <param name="char_replace" type="text" value="_" label="char_replace"
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23 help="Changes the default character used to replace invalid characters found in the mapping file. Must be a valid character (alphanumeric or underscore). NOT IMPLEMENTED CURRENTLY [default: _]"/>
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24 <param name="not_barcoded" type="boolean" truevalue="--not_barcoded" falsevalue="" checked="false" label="not_barcoded"
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25 help="Use -b if barcodes are not present. [default: False]"/>
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26 <param name="variable_len_barcodes" type="boolean" truevalue="--variable_len_barcodes" falsevalue="" checked="false" label="variable_len_barcodes"
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27 help="Use -B if variable length barcodes are present to suppress warnings about barcodes of unequal length. [default: False]"/>
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28 <param name="disable_primer_check" type="boolean" truevalue="--disable_primer_check" falsevalue="" checked="false" label="disable_primer_check"
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29 help="Use -p to disable checks for primers. [default: False]"/>
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30 <param name="verbose" type="boolean" truevalue="" falsevalue="--verbose" checked="false" label="verbose"
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31 help="Turn on this flag to disable verbose output. [default: True]"/>
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32 </inputs>
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33 <outputs>
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34 <data format="txt" name="log"/>
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35 <data format="tabular" name="corrected_mapping" label="${tool.name} on ${on_string}: corrected_mapping"/>
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help>
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40
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41 </help>
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42 </tool>
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