comparison taxonomy_krona_chart.xml @ 1:09552faff9c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit e4c2b31a732b57cc0210070afeaa2dfeca1e1eb4

0:bd565e1e3c5f

<tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.4">kronatools</requirement>
  </requirements>
  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
  <command>
    #if $input.ext == 'taxonomy'
      ktImportGalaxy "${input}" -o "${output}"
    #else
      ktImportText "${input}" -o "${output}"
    #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" />
  </inputs>
  <outputs>
    <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
  </outputs>
  <help>
**What it does**

This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_.
It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools.

.. _Krona: http://sourceforge.net/p/krona/home/krona/

------

**License and citation**

This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

If you use this tool in Galaxy, please cite |Cuccuru2014|_.

.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135

This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_.

.. _Krona: http://sourceforge.net/p/krona/home/krona/
.. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385
.. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385
  </help>
</tool>

1:09552faff9c0

<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.5">krona</requirement>
  </requirements>
  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
  <command>
  <![CDATA[

  #if $type_of_data.input[0].is_of_type('taxonomy'):

        ktImportGalaxy
        -a
        -d "${type_of_data.max_rank}"
        -n "${root_name}"
        -o ${output}
        ${combine_inputs}
        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
            "${input_dataset},${input_count}"
        #end for

  #else:

        ktImportText
        -a
        -n "${root_name}"
        -o ${output}
        ${combine_inputs}
        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
            "${input_dataset},${input_count}"
        #end for

  #end if

  ]]>

  </command>
  <inputs>
    <conditional name="type_of_data">
      <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text">
        <option value="taxonomy" selected="True">Taxonomy</option>
        <option value="text">MetaPhlAn</option>
      </param>
      <when value="taxonomy">
        <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
        <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
            <option value="8">Class</option> 
            <option value="0">Show entire tree</option>
            <option value="1">Superkingdom</option>
            <option value="2">Kingdom</option>
            <option value="3">Subkingdom</option>
            <option value="4">Superphylum</option>
            <option value="5">Phylum</option>
            <option value="6">Subphylum</option>
            <option value="7">Superclass</option>
            <option value="9">Subclass</option>
            <option value="10">Superorder</option>
            <option value="11">Order</option>
            <option value="12">Suborder</option>
            <option value="13">Superfamily</option>
            <option value="14">Family</option>
            <option value="15">Subfamily</option>
            <option value="16">Tribe</option>
            <option value="17">Subtribe</option>
            <option value="18">Genus</option>
            <option value="19">Subgenus</option>
            <option value="20">Species</option>
            <option value="21">Subspecies</option>
        </param>
      </when>
      <when value="text">
        <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
      </when>
    </conditional>
    <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
    <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
  </inputs>
  <outputs>
    <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
  </outputs>
  <tests>
    <test>
      <param name="type_of_data_selector" value="taxonomy"/>
      <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
      <param name="max_rank" value="Genus"/>
      <param name="root_name" value="Root"/>
      <param name="combine_inputs" value="False"/>
      <output name="output" file="krona_test1.html" ftype="html" lines_diff="100"/>
    </test>
  </tests>
  <help>
**What it does**

This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 


.. _Krona: http://sourceforge.net/p/krona/home/krona/

------

**Krona options**

The Galaxy version supports the following options::
                                                                                                                                                                                      
  -n   Name of the highest level.
  -c   Combine data from each file, rather than creating separate datasets within the chart.
  -d   Maximum depth of wedges to include in the chart.

-----

**License and citation**

This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

You can use this tool only if you agree to the license terms of: `Krona`_.

.. _Krona: http://sourceforge.net/p/krona/home/krona/


  </help>
  <citations>
        <citation type="doi">10.1186/1471-2105-12-385</citation>
        <citation type="doi">10.1093/bioinformatics/btu135</citation>
    </citations>
</tool>