comparison pe_histogram.xml @ 3:bd1416eea1f0 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 4731e16b619f4ea176b6f68e34b8f9f9ac1a776c"

2:9be99db0304a

<tool id="pe_histogram" name="Paired-end histogram" version="1.0.1">
    <description>of insert size frequency</description>
    <requirements>
        <requirement type="package" version="8.0.112">openjdk</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
ln -s '${input_bam}' localbam.bam &&
ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
java -jar '$__tool_directory__/PEHistogram.jar'

-t '$output2'
1>/dev/null
    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
        <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
    </inputs>
    <outputs>
        <data name="output1" format="png" />
        <data name="output2" format="tabular" />
    </outputs>

3:bd1416eea1f0

<tool id="pe_histogram" name="Paired-end histogram" version="1.0.1">
    <description>of insert size frequency</description>
    <requirements>
        <requirement type="package" version="11.0.1">openjdk</requirement>
        <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
ln -s '${input_bam}' localbam.bam &&
ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
java -jar '$__tool_directory__/PEHistogram.jar'

-t '$output2'
1>/dev/null
    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="lower_limit" type="integer" value="" optional="true" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
        <param name="upper_limit" type="integer" value="" optional="true" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
    </inputs>
    <outputs>
        <data name="output1" format="png" />
        <data name="output2" format="tabular" />
    </outputs>