view qiime/collate_alpha.xml @ 0:9e12a0762f87 draft

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<tool id="collate_alpha" name="collate_alpha" version="1.2.0">
 <description>Collate alpha diversity results</description>
 <requirements>
  <requirement type="binary">collate_alpha.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir=$output1.extra_files_path
  --galaxy_new_files_path='$__new_file_path__'
  --galaxy_logfile=$output1
  --galaxy_new_datasets='^\S+\.txt$:txt'
  --galaxy_datasetid=$output1.id
  collate_alpha.py
  --input_path=$input_path.extra_files_path
  --output_path='$__new_file_path__'
 </command>
 <inputs>
  <param name="input_path" type="data" format="txt"  label="input_path"
   help="Input is alpha diversity log file [REQUIRED]"/>
  <!--<param name="example_path" type="text"  label="example_path"
   help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>-->
 </inputs>
 <outputs>
  <data format="txt" name="output1" label="${tool.name} on ${on_string}"/>
 </outputs>
 <tests>
 </tests>
 <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files.
 </help>
</tool>