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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="denoise" name="denoise" version="1.2.0">
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2 <description>Denoise a flowgram file</description>
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3 <requirements>
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4 <requirement type="binary">denoise.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='$__new_file_path__'
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9 denoise.py
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10 --input_file=$input_file
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11 --fasta_file=$fasta_file
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12 --output_dir=$__new_file_path__
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13 --method=$method
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14 $keep_intermediates
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15 --cut-off=$cut_off
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16 --precision=$precision
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17 --num_cpus=$num_cpus
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18 $force_overwrite
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19 --map_fname=$map_fname
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20 --primer=$primer
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21 </command>
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22 <inputs>
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23 <param name="input_file" type="data" format="txt" label="input_file"
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24 help="path to flowgram files (.sff.txt), comma separated [REQUIRED]"/>
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25 <param name="fasta_file" type="data" format="fasta" label="fasta_file"
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26 help="path to fasta file from split_libraries.py [REQUIRED]"/>
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27 <param name="method" type="text" value="fast" label="method"
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28 help="Method to use for denoising. Choice of pyronoise or fast [default: fast]"/>
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29 <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
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30 help="Do not delete intermediate files -- useful for debugging [default: False]"/>
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31 <param name="cut_off" type="float" value="0.05" label="cut-off"
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32 help="cut-off value (passed to pyroNoise) [default: 0.05]"/>
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33 <param name="precision" type="float" value="15.0" label="precision"
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34 help="precision (passed to pyroNoise)[default: 15.0]"/>
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35 <param name="num_cpus" type="integer" value="1" label="num_cpus"
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36 help="number of CPUs [default: 1]"/>
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37 <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
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38 help="Overwrite files in output directory [default: False]"/>
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39 <param name="map_fname" type="data" format="tabular" label="map_fname"
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40 help="name of mapping file, Has to contain field LinkerPrimerSequence. [REQUIRED] when method is fast"/>
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41 <param name="primer" type="text" label="primer"
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42 help="primer sequence [default: %default]"/>
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43 </inputs>
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44 <outputs>
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45
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46 </outputs>
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47 <tests>
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48 </tests>
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49 <help>
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50
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51 </help>
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52 </tool>
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