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comparison plot_rank_abundance_graph.xml @ 0:e5c3175506b7 default tip

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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="plot_rank_abundance_graph" name="plot_rank_abundance_graph" version="1.2.0">
2 <description>plot rank-abundance curve</description>
3 <requirements>
4 <requirement type="binary">plot_rank_abundance_graph.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 plot_rank_abundance_graph.py
10 --otu_table_fp=$otu_table_fp
11 --sample_name=$sample_name
12 --output_dir=$__new_file_path__
13 $absolute_counts
14 $no_legend
15 $x_linear_scale
16 $y_linear_scale
17 --file_type=$file_type
18 </command>
19 <inputs>
20 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
21 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
22 <param name="sample_name" type="text" label="sample_name"
23 help="name of the sample to plot. Use '*' to plot all. [REQUIRED]"/>
24 <param name="absolute_counts" type="boolean" truevalue="--absolute_counts" falsevalue="" checked="false" label="absolute_counts"
25 help="plot absolute abundance values instead of relative [default: False]"/>
26 <param name="no_legend" type="boolean" truevalue="--no-legend" falsevalue="" checked="false" label="no-legend"
27 help="do not draw a legend [default: False]"/>
28 <param name="x_linear_scale" type="boolean" truevalue="--x_linear_scale" falsevalue="" checked="false" label="x_linear_scale"
29 help="draw x axis in linear scale [default: False]"/>
30 <param name="y_linear_scale" type="boolean" truevalue="--y_linear_scale" falsevalue="" checked="false" label="y_linear_scale"
31 help="draw y axis in linear scale [default: False]"/>
32 <param name="file_type" type="text" value="pdf" label="file_type"
33 help="save plot using this image type. Choice of pdf, svg, png, eps [default: pdf]"/>
34 </inputs>
35 <outputs>
36
37 </outputs>
38 <tests>
39 </tests>
40 <help>
41
42 </help>
43 </tool>
44