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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="quality_scores_plot" name="quality_scores_plot" version="1.2.1">
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2 <description>Generates histograms of sequence quality scores and number of nucleotides recorded at a particular index</description>
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3 <requirements>
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4 <requirement type="binary">quality_scores_plot.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='$__new_file_path__'
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9 quality_scores_plot.py
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10 --qual_fp=$qual_fp
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11 --output_dir=$__new_file_path__
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12 --score_min=$score_min
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13 --verbose
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14 </command>
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15 <inputs>
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16 <param name="qual_fp" type="data" format="qual" label="qual_fp"
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17 help="Quality score file used to generate histogram data. [REQUIRED]"/>
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18 <param name="score_min" type="text" value="25" label="score_min"
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19 help="Minimum quality score to be considered acceptable. Used to draw dotted line on histogram for easy visualization of poor quality scores. [default: 25]"/>
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20 </inputs>
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21 <outputs>
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22
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23 </outputs>
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24 <tests>
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25 </tests>
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26 <help>
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27
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28 </help>
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29 </tool>
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