comparison kraken-filter.xml @ 1:7dfb0218e838 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 3abfc7eb2999fa588862b84c453012c811fa8350

0:cbb802a726fd

<tool id="kraken-filter" name="Kraken-filter" version="1.1.0">
    <description>
        filter classification by confidence score
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>
        <![CDATA[
        @SET_DATABASE_PATH@ &&
        kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
        ]]>

        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="filtered_output" />
    </outputs>
    <help>
<![CDATA[

.. class:: warningmark

 the last 3 k-mers mapped to taxonomy ID #562

In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
    ]]>
    </help>
    <expand macro="version_command" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="citations" />
</tool>

1:7dfb0218e838

<tool id="kraken-filter" name="Kraken-filter" version="1.2.0">
    <description>
        filter classification by confidence score
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        <![CDATA[
        @SET_DATABASE_PATH@ &&
        kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
        ]]>

        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="filtered_output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="kraken_filter_test1.tab"/>
            <param name="threshold" value="0"/>
            <param name="kraken_database" value="test_db"/>
            <output name="output" file="kraken_filter_test1_output.tab" ftype="tabular"/>
        </test>
    </tests>

    <help>
<![CDATA[

.. class:: warningmark

 the last 3 k-mers mapped to taxonomy ID #562

In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
    ]]>
    </help>
    <expand macro="citations" />
</tool>