comparison plot_rank_abundance_graph.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

0:e5c3175506b7

<tool id="plot_rank_abundance_graph" name="plot_rank_abundance_graph" version="1.2.0">
 <description>plot rank-abundance curve</description>
 <requirements>
  <requirement type="binary">plot_rank_abundance_graph.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  plot_rank_abundance_graph.py
  --otu_table_fp=$otu_table_fp
  --sample_name=$sample_name
  --output_dir=$__new_file_path__
  $absolute_counts
  $no_legend
  $x_linear_scale
  $y_linear_scale
  --file_type=$file_type
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
   help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
  <param name="sample_name" type="text"  label="sample_name"
   help="name of the sample to plot. Use '*' to plot all. [REQUIRED]"/>
  <param name="absolute_counts" type="boolean" truevalue="--absolute_counts" falsevalue="" checked="false" label="absolute_counts"
   help="plot absolute abundance values instead of relative [default: False]"/>
  <param name="no_legend" type="boolean" truevalue="--no-legend" falsevalue="" checked="false" label="no-legend"
   help="do not draw a legend [default: False]"/>
  <param name="x_linear_scale" type="boolean" truevalue="--x_linear_scale" falsevalue="" checked="false" label="x_linear_scale"
   help="draw x axis in linear scale [default: False]"/>
  <param name="y_linear_scale" type="boolean" truevalue="--y_linear_scale" falsevalue="" checked="false" label="y_linear_scale"
   help="draw y axis in linear scale [default: False]"/>
  <param name="file_type" type="text" value="pdf" label="file_type"
   help="save plot using this image type. Choice of pdf, svg, png, eps [default: pdf]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>