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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="plot_rank_abundance_graph" name="plot_rank_abundance_graph" version="1.2.0">
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2 <description>plot rank-abundance curve</description>
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3 <requirements>
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4 <requirement type="binary">plot_rank_abundance_graph.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='$__new_file_path__'
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9 plot_rank_abundance_graph.py
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10 --otu_table_fp=$otu_table_fp
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11 --sample_name=$sample_name
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12 --output_dir=$__new_file_path__
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13 $absolute_counts
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14 $no_legend
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15 $x_linear_scale
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16 $y_linear_scale
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17 --file_type=$file_type
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18 </command>
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19 <inputs>
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20 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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21 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
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22 <param name="sample_name" type="text" label="sample_name"
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23 help="name of the sample to plot. Use '*' to plot all. [REQUIRED]"/>
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24 <param name="absolute_counts" type="boolean" truevalue="--absolute_counts" falsevalue="" checked="false" label="absolute_counts"
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25 help="plot absolute abundance values instead of relative [default: False]"/>
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26 <param name="no_legend" type="boolean" truevalue="--no-legend" falsevalue="" checked="false" label="no-legend"
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27 help="do not draw a legend [default: False]"/>
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28 <param name="x_linear_scale" type="boolean" truevalue="--x_linear_scale" falsevalue="" checked="false" label="x_linear_scale"
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29 help="draw x axis in linear scale [default: False]"/>
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30 <param name="y_linear_scale" type="boolean" truevalue="--y_linear_scale" falsevalue="" checked="false" label="y_linear_scale"
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31 help="draw y axis in linear scale [default: False]"/>
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32 <param name="file_type" type="text" value="pdf" label="file_type"
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33 help="save plot using this image type. Choice of pdf, svg, png, eps [default: pdf]"/>
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34 </inputs>
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35 <outputs>
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36
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37 </outputs>
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38 <tests>
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39 </tests>
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40 <help>
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41
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42 </help>
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43 </tool>
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