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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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1 <tool id="transform_coordinate_matrices" name="transform_coordinate_matrices" version="1.2.0">
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2 <description>Transform 2 coordinate matrices</description>
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3 <requirements>
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4 <requirement type="binary">transform_coordinate_matrices.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='$__new_file_path__'
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9 transform_coordinate_matrices.py
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10 --input_fps=$input_fps
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11 --output_dir=$__new_file_path__
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12 --random_trials=$random_trials
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13 --num_dimensions=$num_dimensions
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14 --sample_id_map_fp=$sample_id_map_fp
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15 $store_trial_details
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16 </command>
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17 <inputs>
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18 <param name="input_fps" type="text" label="input_fps"
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19 help="comma-separated input files [REQUIRED]"/>
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20 <param name="random_trials" type="integer" value="-1" label="random_trials"
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21 help="Number of random permutations of matrix2 to perform. [default: (no Monte Carlo analysis performed)]"/>
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22 <param name="num_dimensions" type="integer" value="-1" label="num_dimensions"
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23 help="Number of dimensions to include in output matrices [default: Consider all dimensions]"/>
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24 <param name="sample_id_map_fp" type="data" format="tabular" label="sample_id_map_fp"
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25 help="Map of original sample ids to new sample ids [default: %default]"/>
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26 <param name="store_trial_details" type="boolean" truevalue="--store_trial_details" falsevalue="" checked="false" label="store_trial_details"
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27 help="Store PC matrices for individual trials [default: False]"/>
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28 </inputs>
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29 <outputs>
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30
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31 </outputs>
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32 <tests>
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33 </tests>
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34 <help>
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35
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36 </help>
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37 </tool>
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