comparison kraken_taxonomy_report.xml @ 2:528a1d91b066 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

1:b97694b21bc3

    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command>python ${__tool_directory__}/kraken_taxonomy_report.py --version</version_command>
    <command>
<![CDATA[

#for $input_classification in $classification:
    ln -s "${input_classification}" "${input_classification.element_identifier}" &&
#end for

export KRAKEN_DB_PATH="${kraken_database.fields.path}" && 
python ${__tool_directory__}/kraken_taxonomy_report.py

--db "${kraken_database.fields.name}"
${show_zeros}
${header_line}
${otu_name}
${taxonomy}
${show_rank}
${intermediate}
${sanitize_names}
#if str( $cluster.cluster ):
    --cluster "${cluster.cluster}"
#else:
    ${cluster.summation}
#end if

--output "${output_report}"

#if $output_tree:
    --output-tree "${output_tree}"
#end if

#for $input_classification in $classification:
    "${input_classification.element_identifier}"
#end for

]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
        <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
        <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
        <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">

            <param name="tree" value="True"/>
            <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
            <output name="output_tree" file="output_tree_3.newick" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: warningmark

**Note**: the database used must be the same as the one used in the original Kraken run

-----

**Output**

The output is tab-delimited, with one line per taxon.

Will optionally output a newick tree built from the kraken database taxonomy using the specified options. Tree branch lengths will be set to "1.00000".


]]>
    </help>
    <citations>
        <citation type="bibtex">@unpublished{Kraken-Taxonomy-Report:2016,
          title  = "Kraken Taxonomy Report",
          author = "Daniel Blankenberg",
          url    = "https://github.com/blankenberg/Kraken-Taxonomy-Report",

2:528a1d91b066

    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command>
    <command><![CDATA[
#for $input_classification in $classification:
    ln -s "${input_classification}" "${input_classification.element_identifier}" &&
#end for

export KRAKEN_DB_PATH='${kraken_database.fields.path}' &&
python '${__tool_directory__}/kraken_taxonomy_report.py'

--db '${kraken_database.fields.name}'
${show_zeros}
${header_line}
${otu_name}
${taxonomy}
${show_rank}
${intermediate}
${sanitize_names}
#if str( $cluster.cluster ):
    --cluster ${cluster.cluster}
#else:
    ${cluster.summation}
#end if

--output '${output_report}'

#if $output_tree:
    --output-tree '${output_tree}'
#end if

#for $input_classification in $classification:
    '${input_classification.element_identifier}'
#end for
    ]]></command>
    <inputs>
        <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
        <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
        <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
        <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">

            <param name="tree" value="True"/>
            <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
            <output name="output_tree" file="output_tree_3.newick" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: warningmark

**Note**: the database used must be the same as the one used in the original Kraken run

-----

**Output**

The output is tab-delimited, with one line per taxon.

Will optionally output a newick tree built from the kraken database taxonomy using the specified options. Tree branch lengths will be set to "1.00000".
    ]]></help>
    <citations>
        <citation type="bibtex">@unpublished{Kraken-Taxonomy-Report:2016,
          title  = "Kraken Taxonomy Report",
          author = "Daniel Blankenberg",
          url    = "https://github.com/blankenberg/Kraken-Taxonomy-Report",