--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crossmap_bam.xml	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,136 @@
+<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
+    <description>Convert genome coordinates or annotation files between genome assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        #if $input_file.extension == "bam":
+            #set $input_file = "input.sam"
+            samtools view -h '${seq_source.input}' > '${input_file}' &&
+        #else:
+            #set $input_file = "input.bam"
+            ln -s '${seq_source.input}' '${input_file}'
+        #end if
+
+        CrossMap.py
+            bam
+
+            "$chain_source.input_chain"
+            $optional_tags
+
+            -m $insert_size
+            -s $insert_size_stdev
+            -t $insert_size_fold
+
+            '${input_file}'
+            '${output}'
+
+            && samtools sort "${output}.sam" > '${output}'
+            && samtools sort "${output}.unmap.sam" > '${output_unmapped}'
+    ]]></command>
+
+    <inputs>
+        <conditional name="seq_source">
+            <expand macro="source" />
+            <when value="cached">
+                <param type="data" format="bam" name="input" label="BAM file">
+                    <validator type="unspecified_build"/>
+                    <!-- Gives error in tests
+                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
+                    -->
+                </param>
+                <param name="input_chain" type="select" label="Lift Over To">
+                    <options from_file="liftOver.loc">
+                        <column name="name" index="1"/>
+                        <column name="value" index="2"/>
+                        <column name="dbkey" index="0"/>
+                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" format="bam" name="input" label="BAM/SAM file"/>
+                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+        <expand macro="chain" />
+        <param name="optional_tags" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM/SAM Headers" argument="-a"/>
+
+        <param name="insert_size" type="float" value="200.0" label="Insert size" argument="-m" help="Average insert size of pair-end sequencing (bp) [default=200.0]"/>
+        <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev" argument="-s" help="Stanadard deviation of insert size. [default=30.0]"/>
+        <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange" argument="-t" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]"/>
+</inputs>
+
+    <outputs>
+        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
+        <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
+    </outputs>
+
+    <tests>
+    <!-- BAM/SAM -->
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+
+            <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
+            <output name="output_unmapped" file="test_bam_01_output_a.unmap.bam" compare="diff" lines_diff="8"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+SAM / BAM
+---------
+
+    CrossMap updates chromosomes, genome coordinates, header sections, and all
+    SAM flags accordingly. The program version (of CrossMap) is inserted into the
+    header section, along with the names of the original BAM file and the chain
+    file. For pair-end sequencing, insert size is also recalculated.
+
+
+    **Optional tags**
+
+    Q
+      QC. QC failed.
+
+    N
+      Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
+
+    M
+      Multiple mapped. Alignment can be liftover to multiple places.
+
+    U
+      Unique mapped. Alignment can be liftover to only 1 place.
+
+    **Tags for pair-end sequencing include:**
+
+    QF = QC failed
+    NN = both read1 and read2 unmapped
+    NU = read1 unmapped, read2 unique mapped
+    NM = read1 unmapped, multiple mapped
+    UN = read1 uniquely mapped, read2 unmap
+    UU = both read1 and read2 uniquely mapped
+    UM = read1 uniquely mapped, read2 multiple mapped
+    MN = read1 multiple mapped, read2 unmapped
+    MU = read1 multiple mapped, read2 unique mapped
+    MM = both read1 and read2 multiple mapped
+
+    **Tags for single-end sequencing include**
+
+    QF = QC failed
+    SN = unmaped
+    SM = multiple mapped
+    SU = uniquely mapped
+
+See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details
+]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>