SHAMAN.xml

<tool id="SHAMAN" name="SHAMAN">
  <!--This tool descriptor has been generated by ToolDog v0.3.0-->
  <!--Information was obtained from the Galaxy instance: https://usegalaxy.org v17.01 and EDAM v1.16-->
  <description>SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization.</description>
  <edam_operations>
    <edam_operation>operation_0337</edam_operation>
    <edam_operation>operation_3435</edam_operation>
    <edam_operation>operation_3223</edam_operation>
    <edam_operation>operation_3221</edam_operation>
  </edam_operations>
  <edam_topics>
    <edam_topic>topic_3174</edam_topic>
  </edam_topics>
  <stdio>
    <exit_code level="fatal" range="1:"/>
  </stdio>
  <version_command>COMMAND --version</version_command>
  <command><![CDATA[COMMAND --INPUT1 $INPUT1]]></command>
  <inputs>
    <param argument="INPUT1" format="tabular" label="Report" name="INPUT1" type="data">
      <!--This parameter has been automatically generated from https://bio.tools/tool/SHAMAN by ToolDog v0.3.0.-->
      <!--FIXME: Please map this parameter to its command line argument.-->
    </param>
  </inputs>
  <outputs>
    <data format="data" from_work_dir="OUTPUT1.data" hidden="false" name="OUTPUT1">
      <!--This parameter has been automatically generated from https://bio.tools/tool/SHAMAN by ToolDog v0.3.0.-->
      <!--FIXME: Please map this parameter to its command line argument.-->
    </data>
  </outputs>
  <help><![CDATA[

What it is ?
============

SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization.

SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016] . SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014] . Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995]. The PCOA is performed with the ade4 R package and plots are generated with ggplot2 or D3.js packages. SHAMAN is compatible with standard formats for metagenomic analysis.

External links:
===============

- Tool homepage_
- bio.tools_ entry

.. _homepage: http://shaman.c3bi.pasteur.fr/
.. _bio.tools: https://bio.tools/tool/SHAMAN]]></help>
  <citations>
    <citation type="doi">10.1073/pnas.1523899113</citation>
  </citations>
</tool>