diff samtools_bam_to_cram.xml @ 0:f11c1dd0b4ae draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit fdc0553f8451316c1f0b63488db3ef250e99b3ad

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_bam_to_cram.xml	Fri May 05 13:12:05 2017 -0400
@@ -0,0 +1,125 @@
+<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="1.2.0">
+    <description>convert BAM alignments to CRAM format</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        #if str( $input_alignment.metadata.bam_index ) != "None":
+            ln
+                -f
+                -s
+                '${input_alignment.metadata.bam_index}'
+                '${input_alignment}.bai'
+                &&
+        #end if
+
+        samtools view
+            #if $parameter_regions.target_region == "regions_bed_file"
+                -L '${parameter_regions.regions_bed_file}'
+            #end if
+
+            -@\${GALAXY_SLOTS:-1}
+            -C
+            -T '${reference_source.input_reference}'
+            -o '${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="bam,sam" label="BAM (or SAM) 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" format="fasta" label="Genome reference FASTA file">
+                    <options from_data_table="all_fasta">
+                        <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="Genome 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" type="data" format="bed"
+                       label="only include reads overlapping this BED FILE" argument="-L"/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="cram" name="output_alignment" label="$tool.name on ${on_string}.cram"></data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_alignment" value="test.bam" ftype="bam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="input_reference" 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_alignment" value="test.sam" ftype="sam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="input_reference" 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_alignment" value="test.bam" ftype="bam" />
+            <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.cram"  compare="sim_size" delta="250" />
+        </test>
+        <test>
+            <param name="input_alignment" value="test.bam" ftype="bam" />
+            <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.cram"  compare="sim_size" delta="250" />
+        </test>
+    </tests>
+
+    <help>
+
+**What this tool does**
+
+Converts alignments from the BAM format to the CRAM format using the SAMTools_ toolkit. The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient.
+
+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+    </help>
+
+    <expand macro="citations" />
+</tool>