# HG changeset patch
# User iuc
# Date 1482178720 18000
# Node ID aa72470e14f7a5de359bc95f25d51b271a19c994

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687

diff -r 000000000000 -r aa72470e14f7 samblaster.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samblaster.xml	Mon Dec 19 15:18:40 2016 -0500
@@ -0,0 +1,211 @@
+<tool id="samblaster" name="samblaster" version="0.1.24">
+    <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
+    <requirements>
+        <requirement type="package" version="0.1.24">samblaster</requirement>
+        <requirement type="package" version="0.6.5">sambamba</requirement>
+    </requirements>
+    <version_command>samblaster --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input.is_of_type('sam'):
+        #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input
+        #else:
+            #set stream="'%s'" % $input
+        #end if
+        sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) |
+        samblaster
+        $output
+        $discordantFile
+        $splitterFile
+        $unmappedFile
+        $acceptDupMarks
+        $excludeDups
+        $removeDups
+        $addMateTags
+        $compatibility_mode
+        --maxSplitCount '$maxSplitCount'
+        --maxUnmappedBases '$maxUnmappedBases'
+        --minIndelSize '$minIndelSize'
+        --minNonOverlap '$minNonOverlap'
+        --minClipSize '$minClipSize'
+        #if $output != "-o /dev/null":
+            && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam)
+        #end if
+        #if $discordantFile:
+            && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam)
+        #end if
+        #if $splitterFile:
+            && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam)
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="bam,sam"/>
+        <param argument="--output" label="Output bam file for all input alignments" type="boolean" checked="true" truevalue="-o output.sam" falsevalue="-o /dev/null"/>
+        <param argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/>
+        <param argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/>
+        <param argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>
+        <param argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/>
+        <param argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/>
+        <param argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/>
+        <param argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>
+        <param name="compatibility_mode" argument="-M" label="Run in compatibility mode?" help="Both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option." type="boolean" truevalue="-M" falsevalue="" />
+        <param argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/>
+        <param argument="--maxUnmappedBases" label="Maximum number of un-aligned bases between two alignments to be included in splitter file." type="integer" value="50" min="1"/>
+        <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/>
+        <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/>
+        <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/>
+    </inputs>
+    <outputs>
+        <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam">
+            <filter>output</filter>
+        </data>
+        <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam">
+            <filter>discordantFile</filter>
+        </data>
+        <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam">
+            <filter>splitterFile</filter>
+        </data>
+        <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq">
+            <filter>unmappedFile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sr.input.bam"/>
+            <param name="output" value="true"/>
+            <param name="discordandFile" value="false"/>
+            <param name="splitterFile" value="true"/>
+            <param name="unmappedFile" value="true"/>
+            <output name="output_bam" file="output.bam" compare="sim_size"/>
+            <output name="splitter_bam" file="splitters.bam" compare="sim_size"/>
+            <output name="unmapped_fastq">
+                <assert_contents>
+                    <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="sr.input.sam.gz" ftype="sam"/>
+            <param name="output" value="true"/>
+            <param name="discordandFile" value="false"/>
+            <param name="splitterFile" value="true"/>
+            <param name="unmappedFile" value="true"/>
+            <output name="output_bam" file="output.bam" compare="sim_size"/>
+            <output name="splitter_bam" file="splitters.bam" compare="sim_size"/>
+            <output name="unmapped_fastq">
+                <assert_contents>
+                    <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" />
+                </assert_contents>
+            </output>
+         </test>
+    </tests>
+    <help><![CDATA[
+
+*samblaster*
+============
+
+Summary
+-------
+
+*samblaster* is a fast and flexible program for marking duplicates in
+**read-id grouped** paired-end SAM files. It can also optionally output
+discordant read pairs and/or split read mappings to separate SAM files,
+and/or unmapped/clipped reads to a separate FASTQ file. When marking
+duplicates, *samblaster* will require approximately 20MB of memory per
+1M read pairs.
+
+Usage
+-----
+
+See the `SAM File Format
+Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__ for details
+about the SAM alignment format.
+
+By default, samblaster marks duplicates with SAM FLAG 0x400. The
+**--removeDups** option will instead remove duplicate alignments from the
+output file.
+
+**ALIGNMENT TYPE DEFINITIONS:** Below, we will use the following
+definitions for alignment types. Starting with *samblaster* release
+0.1.22, these definitions are affected by the use of the **-M** option.
+By default, *samblaster* will use the current definitions of alignment
+types as specified in the `SAM
+Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__. Namely,
+alignments marked with FLAG 0x100 are considered *secondary*, while
+those marked with FLAG 0x800 are considered *supplemental*. If the
+**-M** option is specified, alignments marked with either FLAG 0x100 or
+0x800 are considered *supplemental*, and no alignments are considered
+*secondary*. A *primary* alignment is always one that is neither
+*secondary* nor *supplemental*. Only *primary* and *supplemental*
+alignments are used to find chimeric (split-read) mappings. The **-M**
+flag is used for backward compatibility with older SAM/BAM files in
+which "chimeric" alignments were marked with FLAG 0x100, and should also
+be used with output from more recent runs of *bwa mem* using its **-M**
+option.
+
+**DISCORDANT READ PAIR IDENTIFICATION:** A **discordant** read pair is
+one which meets all of the following criteria:
+
+1. Both side of the read pair are mapped (neither FLAG 0x4 or 0x8 is
+   set).
+2. The *properly paired* FLAG (0x2) is not set.
+3. *Secondary* or *supplemental* alignments are never output as
+   discordant, although a discordant read pair can have such alignments
+   associated with them.
+4. Duplicate read pairs that meet the above criteria will be output as
+   discordant unless the **-e** option is used.
+
+**UNMAPPED/CLIPPED READ IDENTIFICATION:** An **unmapped** or **clipped**
+read is a *primary* alignment that is unaligned over all or part of its
+length respectively. The lack of a full alignment may be caused by a SV
+breakpoint that falls within the read. Therefore, *samblaster* will
+optionally output such reads to a FASTQ file for re-alignment by a tool,
+such as `YAHA <https://github.com/GregoryFaust/yaha/>`__, geared toward
+finding split-read mappings. *samblaster* applies the following strategy
+to identify and output unmapped/clipped reads:
+
+1. An **unmapped** read has the *unmapped read* FLAG set (0x4).
+2. A **clipped** read is a mapped read with a CIGAR string that begins
+   or ends with at least **--minClipSize** unaligned bases (CIGAR code S
+   and/or H), and is not from a read that has one or more *supplemental*
+   alignments.
+3. In order for *samblaster* to output the entire sequence for clipped
+   reads, the input SAM file must have soft clipped primary alignments.
+4. *samblaster* will output unmapped/clipped reads into a FASTQ file if
+   QUAL information is available in the input file, and a FASTA file if
+   not.
+5. Unmapped/clipped reads that are part of a duplicate read pair will be
+   output unless the **-e** option is used.
+
+
+**Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab,
+University of Virginia <http://faculty.virginia.edu/irahall/>`__
+
+**Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast
+duplicate marking and structural variant read extraction,”
+*Bioinformatics* Sept. 2014; **30**\ (17):
+2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__
+
+**Also see:** `SAMBLASTER\_Supplemental.pdf
+<https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__
+for additonal discussion and statistics about the duplicates marked by
+*samblaster* vs. *Picard* using the NA12878 sample dataset. Click the
+preceeding link or download the file from this repository.
+**Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab,
+University of Virginia <http://faculty.virginia.edu/irahall/>`__
+
+**Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast
+duplicate marking and structural variant read extraction,”
+*Bioinformatics* Sept. 2014; **30**\ (17):
+2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__
+
+**Also see:** `SAMBLASTER\_Supplemental.pdf
+<https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__
+for additonal discussion and statistics about the duplicates marked by
+*samblaster* vs. *Picard* using the NA12878 sample dataset. Click the
+preceeding link or download the file from this repository.
+
+   ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu314</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r aa72470e14f7 test-data/output.bam
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diff -r 000000000000 -r aa72470e14f7 test-data/splitters.bam
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diff -r 000000000000 -r aa72470e14f7 test-data/sr.input.bam
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diff -r 000000000000 -r aa72470e14f7 test-data/sr.input.sam.gz
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