comparison leftalign.xml @ 35:a5937157062f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 84c34980b4fd8454c1cc630be5d6a3c22a4a1ef3"

34:a7c9782130e8

        <test>
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
            <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
            <param name="iterations" value="5"/>
            <output name="output_bam" file="left-align-output.bam" />
        </test>
    </tests>
    <help>

When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.

35:a5937157062f

        <test>
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
            <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
            <param name="iterations" value="5"/>
            <output name="output_bam" file="left-align-output.bam" ftype="bam" lines_diff="2" />
        </test>
    </tests>
    <help>

When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.