--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_cram_to_bam.xml	Tue May 09 11:18:56 2017 -0400
@@ -0,0 +1,117 @@
+<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@">
+    <description>convert CRAM alignments to BAM format</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        #if str( $input_alignment.metadata.cram_index ) != "None":
+            ln -f -s '${input_alignment.metadata.cram_index}' '${input_alignment}.crai' &&
+        #end if
+
+        #if $reference_source.reference_source_selector == 'history':
+            #set ref_fa = 'ref.fa'
+            ln -s '${reference_source.input_reference}' ref.fa &&
+        #else:
+            #set ref_fa = str( $reference_source.input_reference.fields.path )
+        #end if
+
+        samtools view
+            #if $parameter_regions.target_region == "regions_bed_file"
+                -L '${parameter_regions.regions_bed_file}'
+            #end if
+            -@ \${GALAXY_SLOTS:-2}
+            -b
+            -T '$ref_fa'
+            -o '$output_alignment'
+            '$input_alignment'
+            #if $parameter_regions.target_region == "region"
+                '${parameter_regions.region_string}'
+            #end if
+    ]]></command>
+
+    <inputs>
+        <param name="input_alignment" type="data" format="cram" label="CRAM alignment file"/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load reference genome from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="input_reference" type="select" label="Reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" />
+                    </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="input_reference" 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>
+            </param>
+            <when value="entire_input_file" />
+            <when value="region">
+                <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" />
+            </when>
+            <when value="regions_bed_file">
+                <param name="regions_bed_file" argument="-L" type="data" format="bed" label="Only include reads overlapping this BED file" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="output_alignment" format="bam" label="$tool.name on ${on_string}.bam"></data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_alignment" value="test.cram" ftype="cram" />
+            <param name="reference_source_selector" value="history" />
+            <param name="input_reference" value="test.fa" />
+
+            <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
+        </test>
+        <test>
+            <param name="input_alignment" value="test.cram" ftype="cram" />
+            <param name="reference_source_selector" value="history" />
+            <param name="input_reference" value="test.fa" />
+            <param name="target_region" value="region" />
+            <param name="region_string" value="CHROMOSOME_I" />
+
+            <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
+        </test>
+        <test>
+            <param name="input_alignment" value="test.cram" ftype="cram" />
+            <param name="reference_source_selector" value="history" />
+            <param name="input_reference" 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.bam" compare="sim_size" delta="250" />
+        </test>
+        <test>
+            <param name="input_alignment" value="test2.cram" dbkey="equCab2" ftype="cram" />
+            <param name="reference_source_selector" value="cached" />
+            <param name="input_reference" value="equCab2chrM" />
+            <param name="target_region" value="entire_input_file" />
+            <output name="output_alignment" file="sam_to_bam_out2.bam" compare="sim_size" delta="250" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What this tool does**
+
+Converts alignments from the CRAM format to the BAM format using the ``samtools view`` command.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>