annotate rdpmulticlassifier/rdp_multi_classifier.xml @ 0:a73ae72b47aa draft default tip

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<tool id="rdpmulticlassifier" name="RDP MultiClassifier" version="1.1">
 <description>Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy</description>
 <command interpreter="bash">
       #if $table.addotutable
         rdpmulticlassifier.sh $gene $table.addotutable $input $otu $conf $hier $assign $otutable $format 
       #else
         rdpmulticlassifier.sh $gene $table.addotutable $input NULL $conf $hier $assign NULL $format
       #end if
 </command>
 <requirements>
    <requirement type="package" version="1.1">rdp_multi_classifier_1.1</requirement>
 </requirements>
 <inputs>
  <param name="gene" type="select" label="Select Gene Trainings Model" help="The Multi-Classifier provides two training models: 16S rRNA or Fungal LSU genes.">
        <option value="16srrna" selected="true">16S rRNA</option>
        <option value="fungallsu">Fungal LSU</option>
  </param>
 <conditional name="table">
  <param name="addotutable" type="boolean" value="true" label="Select to generate an OTU Table" help="This is to complete the intermediate OTU Table generated by the 'Map Reads to OTU' tool of the metagenomics workflow. The intermediate OTU table and relabelled OTUs output files of the 'Map Reads to OTU' tool will be required." />
  <when value="true">
  <param name="input" type="data" format="fasta" label="Relabelled OTU input reads of the 'Map Reads to OTU' tool in FASTA format"/>
  <param name="otu" type="data" format="tabular" label="PRE OTU table of the 'Map Reads to OTU' tool" />
  </when>
  <when value="false">
  <param name="input" type="data" format="fasta" label="Input reads file in FASTA format"/>
  </when>
  </conditional> -->
  <param name="conf" type="float" value="0.8" label="Assignment confidence cutoff" help="Specifies the assignment confidence cutoff used to determine the assignment count in the hierarchical format. Range [0-1], Default is 0.8. For sequences shorter than 250 base pairs, the confidence threshold 50% is recommended to improve classification coverage." />
  <param name="format" type="select" label="Tab delimited output format" help="Please see the description below on the 'Tab delimited output format' options.">
        <option value="allrank" selected="true">allrank</option>
        <option value="fixrank">fixrank</option>
        <option value="db">db</option>
  </param>
 </inputs>
 <outputs>
  <data name="hier" format="tabular" label="${tool.name} on ${on_string}:classification_assignment_hierarchical.tab" />
  <data name="assign" format="tabular" label="${tool.name} on ${on_string}:classification_assignment_details.tab" />
  <data name="otutable" format="tabular" label="${tool.name} on ${on_string}: OTU_Table.tab" >
   <filter>table['addotutable']</filter>
  </data>
 </outputs>
 <help>
===========
Description
===========

The RDP MultiClassifier allows rapid Assignment of rRNA sequences into the new bacterial taxonomy. 
This version of the RDP MultiClassifier allows the completion of the intermediate OTU table generated by the USEARCH - 'Map Reads to OTU' tool of the metagenomics workflow.

-----

-----
Input
-----

**No OTU Table generation selected:**

A) File of reads in FASTA format.

.. class:: infomark

Input sequences should be at least 50bp for accurate results. Uppercase and lowercase formats are allowed.

**OTU Table generations is selected:**

A) Relabelled OTU input reads in FASTA format of the 'Map Reads to OTU' tool.

.. class:: warningmark

Please note the 'relabelled OTU' output of the 'Map Reads to OTU' tool is hidden. To access the hidden output, click on the cog wheel in the upper right corner of the History panel and select 'Include Hidden Datasets'. The output dataset will appear with a dialog box. Follow the instruction in the dialog box and click 'here' to unhide the dataset.


B) Pre-OTU Table of the 'Map Reads to OTU' tool in tabular format.

----------
Parameters
----------

Gene Trainings Model
   RDP naive Bayesian Classifier offers two hierarchy models for 16S rRNA and Fungal LSU genes

OTU Table generation
   For OTU Table generation, check the above checkbox and provide the intermediate OTU table (Pre-OTU Table) and the 'relabelled OTU' input reads of the 'Map Reads to OTU' tool of the metagenomics workflow.

Confidence cutoff
   Used to determine the assignment count in the hierarchial format. Range[0-1], default is 0.8. For sequences shorter than 250 base pairs, the confidence threshold 50% is recommended to improve classification coverage.

Tab delimited output format
   a) allrank: outputs the results for all ranks applied for each sequence: seqname, orientation, taxon name, rank, conf, etc
   b) fixrank: only outputs the results for fixed ranks in order: domain, phylum, class, order, family, genus
   c) db: outputs the seqname, trainset_no, tax_id, conf

------
Output
------

The tool generates 2 or 3 outputs depending if 'OTU Table generations' is selected.

**No OTU Table generation selected:**

(A) Sequence count for each taxon in the hierarchy in tab-format: classification_assignment_hierarchical.tab

(B) Sequence-by-sequence classification results including confidence scores at each level of the hierarchy in tab-format: classification_assignment_details.tab   

**OTU Table generations is selected:**

(A) Sequence count for each taxon in the hierarchy in tab-format: classification_assignment_hierarchical.tab

(B) Sequence-by-sequence classification results including confidence scores at each level of the hierarchy in tab-format: classification_assignment_details.tab

(C) OTU Table in tab-format

-----

=========
Resources
=========

RDP_MultiClassifier_Tutorial_

.. _RDP_MultiClassifier_Tutorial: http://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_MULTICLASSIFIER.html


**Wrapper Author**

QFAB Bioinformatics ([e-mail])

</help>
<tests>
  <test>
    <param name="gene" value="16srrna" />
    <param name="addotutable" value="true" />
    <param name="input" value="otuseqs.fasta" />
    <param name="otu" value="preotu.tab" />
    <param name="conf" value="0.8" />
    <param name="format" value="fixrank" />
    <output name="hier" file="class_hier.tab" ftype="tabular" lines_diff="10" />
    <output name="assign" file="class_detail.tab" ftype="tabular" lines_diff="10" />
    <output name="otutable" file="otu_table.tab" ftype="tabular" lines_diff="10" />
  </test>
</tests>
</tool>