comparison samtools_markdup.xml @ 9:40fa6c240105 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

8:a389f74c3630

        <!-- 5) check that stderr is not swallowed w test data from fixmate  -->
        <test expect_exit_code="1" expect_failure="true">
            <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
            <param name="stats" value="yes"/>
            <assert_stderr>
                <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
            </assert_stderr>
        </test>
        <!-- 6) check optical distance and check -c option -->
        <test expect_num_outputs="1">
            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>

9:40fa6c240105

        <!-- 5) check that stderr is not swallowed w test data from fixmate  -->
        <test expect_exit_code="1" expect_failure="true">
            <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
            <param name="stats" value="yes"/>
            <assert_stderr>
                <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
                <has_line line="samtools markdup: error, unable to assign pair hash key."/>
            </assert_stderr>
        </test>
        <!-- 6) check optical distance and check -c option -->
        <test expect_num_outputs="1">
            <param name="bamfile" value="1_markdup.sam" ftype="sam"/>