<tool id="samtools_slice_bam" name="Slice" version="2.0">
  <description>BAM by genomic regions</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <!-- <code file="samtools_slice_options.py"/> -->
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
    <command>
<![CDATA[
    ln -s "${input_bam}" temp_input.bam &&
    ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai &&

    #if str($slice_method.slice_method_selector) == "bed":
    
        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && 

    #elif str($slice_method.slice_method_selector) == "chr":

        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 
        ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&

    #elif str($slice_method.slice_method_selector) == "man":

        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam 

        #for $region in $slice_method.regions:
            "${region.chrom}:${region.start}-${region.end}"
        #end for

        &&

    #end if

    samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "${output_bam}" unsorted_output.bam
]]>
    </command>
    <inputs>
        <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" />
        <conditional name="slice_method">
            <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?">
                <option value="bed">using a list of intervals from a BED dataset</option>
                <option value="chr">by chromosomes/contigs present in the BAM dataset</option>
                <option value="man">by chromosomes/contigs and coordinates</option>
            </param>
            <when value="bed">
                <param format="bed" label="BED file" name="input_interval" type="data" help="BED datasets can be obtained using &quot;Get Data -> UCSC Main&quot; datasource."/>
            </when>
            <when value="chr">
                <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">

                    <!-- The options tagset below extracts reference names from bam file metadata -->
                    <!-- This will not work with bed files with old style metadata. However this  -->
                    <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
                    <!-- The pencil icon and settind datatype to "bam"                            -->
                    <!-- This change has been commited in the following pull request:             -->
                    <!-- https://github.com/galaxyproject/galaxy/pull/107                         -->

                    <options>
                        <filter type="data_meta" ref="input_bam" key="reference_names" />
                    </options>
                </param>
            </when>
            <when value="man">
                <repeat name="regions" title="Regions" min="1">
                    <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">

                        <!-- See comments above -->

                        <options>
                            <filter type="data_meta" ref="input_bam" key="reference_names" />
                        </options>
                    </param>
                    <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/>
                    <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/>
                </repeat>


            </when>
        </conditional>

    </inputs>
    <outputs>
        <data format="bam" name="output_bam" />
    </outputs>
    <tests>
        <test>
            <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="bed"/>
            <param ftype="bed" name="input_interval" value="bam-slice.bed" />
            <output file="bam-slice-test1.bam" ftype="bam" name="output_bam" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="chr"/>
            <param name="refs" value="chrM" />
            <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
            <param name="slice_method_selector" value="man"/>
            <param name="chrom" value="chrM" />
            <param name="start" value="1" />
            <param name="end" value="1000" />
            <output file="bam-slice-test3.bam" ftype="bam" name="output_bam" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**.

This tool is based on ``samtools view`` command. 

@no-chrom-options@

]]>
  </help>
    <expand macro="citations"></expand>
</tool>