comparison samtools_bam_to_cram.xml @ 4:7d3cd2087698 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

3:3d07b8a6dd8c

<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@">
    <description>convert BAM alignments to CRAM format</description>

    <macros>
        <import>macros.xml</import>
    </macros>

                -L '${parameter_regions.regions_bed_file}'
            #end if

            -@ \$addthreads
	    -C
	    -h 
            -o '${output_alignment}'
            -T '$reffa'
            -t '$reffai'
            --output-fmt-option no_ref
            infile

            #end if
    ]]></command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
        <conditional name="addref_cond">
            <param name="addref_select" type="select" label="Load reference genome from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref" type="select" label="Reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey" />
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref" type="data" format="fasta" label="Reference FASTA file"/>
            </when>
        </conditional>
        <conditional name="parameter_regions">
            <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
                <option value="entire_input_file">Entire BAM alignment file</option>
                <option value="region">Specific region</option>
                <option value="regions_bed_file">List of specific regions (BED file)</option>

        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="entire_input_file" />

            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="entire_input_file" />

            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="region" />
            <param name="region_string" value="CHROMOSOME_I" />

            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="regions_bed_file" />
            <param name="regions_bed_file" value="test.bed" ftype="bed" />

            <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
            <param name="addref_select" value="cached" />
            <param name="ref" value="equCab2chrM" />
            <param name="target_region" value="entire_input_file" />
            <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" />
        </test>
    </tests>

    <help><![CDATA[
**What this tool does**

4:7d3cd2087698

<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>convert BAM alignments to CRAM format</description>

    <macros>
        <import>macros.xml</import>
    </macros>

                -L '${parameter_regions.regions_bed_file}'
            #end if

            -@ \$addthreads
	    -C
	    -h
            -o '${output_alignment}'
            -T '$reffa'
            -t '$reffai'
            --output-fmt-option no_ref
            infile

            #end if
    ]]></command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
        <expand macro="mandatory_reference" argument="-t"/>
        <conditional name="parameter_regions">
            <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
                <option value="entire_input_file">Entire BAM alignment file</option>
                <option value="region">Specific region</option>
                <option value="regions_bed_file">List of specific regions (BED file)</option>

        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="entire_input_file" />
            <output name="output_alignment" file="test_bam.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.sam" ftype="sam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="entire_input_file" />
            <output name="output_alignment" file="test_sam.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="region" />
            <param name="region_string" value="CHROMOSOME_I" />
            <output name="output_alignment" file="test_chr1.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" value="test.bam" ftype="bam" />
            <param name="addref_select" value="history" />
            <param name="ref" value="test.fa" />
            <param name="target_region" value="regions_bed_file" />
            <param name="regions_bed_file" value="test.bed" ftype="bed" />
            <output name="output_alignment" file="test_regions.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
            <param name="addref_select" value="cached" />
            <param name="ref" value="equCab2chrM" />
            <param name="target_region" value="entire_input_file" />
            <output name="output_alignment" file="test2.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
    </tests>

    <help><![CDATA[
**What this tool does**