comparison samtools_calmd.xml @ 0:39472bc02d8d draft

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0:39472bc02d8d

<tool id="samtools_calmd" name="Recalculate" version="1.0.0">
    <description>MD/NM tags and '=' bases</description>
    <requirements>
        <requirement type="package" version="1.0">samtools</requirement>
    </requirements>
    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
    <command><![CDATA[
        #if str( $reference_source.reference_source_selector ) == "history":
            #set ref_fa = 'ref.fa'
            ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
        #else:
            #set ref_fa = str( $reference_source.ref_fasta.fields.path )
        #end if
        samtools calmd
        #if str($option_set.option_sets) == 'advanced':
            $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
        #end if
        -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
    </command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <inputs>
        <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref_fasta" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" column="value" key="dbkey" ref="input_bam" />
                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
            </when>
        </conditional>
        <conditional name="option_set">
            <param name="option_sets" type="select" label="Options">
                <option value="default">Use defaults</option>
                <option value="advanced">Advanced options</option>
            </param>
            <when value="default" />
            <when value="advanced">
                <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
                <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
                <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
                <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="option_sets" value="default" /> 
            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
            <param name="reference_source|reference_source_selector" value="history" />
            <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
        </test>
        <!-- Using the test-data-repo's phiX.fa should produce the same output. -->
        <test>
            <param name="option_sets" value="default" /> 
            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
            <param name="reference_source|reference_source_selector" value="cached" />
            <param name="ref_fasta" value="phiX" />
            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
        </test>
        <test>
            <param name="option_sets" value="advanced" /> 
            <param name="change_identical" value="true" />
            <param name="extended_baq" value="true" />
            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
            <param name="reference_source|reference_source_selector" value="history" />
            <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
        </test>
        <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. -->
        <test>
            <param name="option_sets" value="advanced" /> 
            <param name="change_identical" value="true" />
            <param name="extended_baq" value="true" />
            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
            <param name="reference_source|reference_source_selector" value="cached" />
            <param name="ref_fasta" value="phiX" />
            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
        </test>
    </tests>
    <help>
**What it does**

Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. 

------

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_


If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

        </help>
</tool>