comparison taxonomy_krona_chart.xml @ 2:50f204c82159 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 70d4a2d1563e834d8394dce8017a1f0b7ad74f23

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">

      </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>

**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**

2:50f204c82159

<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.6">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
        -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
        -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

&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" )
  ]]>

  </command>
  <inputs>
    <conditional name="type_of_data">

      </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" 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>

**What it does**

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


.. _Krona: https://github.com/marbl/Krona/wiki

------

**Krona options**