comparison artbio_bam_cleaning.xml @ 12:b0f65f88411f draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning commit 6a7ed08b76a45cfcda4e030163d9f246163934ed

11:6815060fb056

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.7+galaxy4">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.6=hb116620_7">samtools</requirement>
        <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
        <requirement type="package" version="1.3.5=py39hba5d119_3">freebayes</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[

        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
            <filter>specify_outputs == 'calMDandMQ' or specify_outputs == 'both'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="specify_outputs" value="calMDandMQ" />
            <param name="ref_file" value="chr22.fa" />
            <output name="fullfilter" file="full.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="chr22.fa" />
            <param name="specify_outputs" value="both" />
            <output name="calmd" file="calmd.bam" ftype="bam" />
            <output name="fullfilter" file="full.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="specify_outputs" value="just_calMD" />
            <param name="ref_file" value="chr22.fa" />
            <output name="calmd" file="calmd.bam" ftype="bam" />
        </test>
    </tests>
    <help>
ARTbio bam cleaning overview
============================

12:b0f65f88411f

<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.10+galaxy0">
    <description>
        on flags and PCR Duplicates and MD recalibration
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.10=h2e538c0_3">samtools</requirement>
        <requirement type="package" version="0.8.1=hadffe2f_1">sambamba</requirement>
        <requirement type="package" version="1.3.7">freebayes</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[

        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
            <filter>specify_outputs == 'calMDandMQ' or specify_outputs == 'both'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="specify_outputs" value="calMDandMQ" />
            <param name="ref_file" value="chr22.fa" />
            <output name="fullfilter" file="full.bam" ftype="bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="2">
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" value="chr22.fa" />
            <param name="specify_outputs" value="both" />
            <output name="calmd" file="calmd.bam" ftype="bam" lines_diff="4" />
            <output name="fullfilter" file="full.bam" ftype="bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <param name="input_bam" value="chr22_sample.bam" ftype="bam" />
            <param name="reference_source_selector" value="history" />
            <param name="specify_outputs" value="just_calMD" />
            <param name="ref_file" value="chr22.fa" />
            <output name="calmd" file="calmd.bam" ftype="bam" lines_diff="4" />
        </test>
    </tests>
    <help>
ARTbio bam cleaning overview
============================