--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crossmap_bed.xml	Tue Sep 26 05:44:37 2017 -0400
@@ -0,0 +1,133 @@
+<tool id="crossmap_bed" name="CrossMap BED" 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[
+        #set $input_file = str($seq_source.input)
+
+        CrossMap.py bed
+            '${chain_source.input_chain}'
+
+            '${input_file}'
+
+            #if str($include_fails) == "True"
+            >
+            #end if
+
+            '${output}'
+    ]]></command>
+
+
+    <inputs>
+       <conditional name="seq_source">
+            <expand macro="source" />
+
+            <when value="cached">
+                <param format="bed" name="input" type="data" label="BED file"
+                       help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
+                    <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>
+            </when>
+            <when value="history">
+                <param type="data" format="bed" name="input" label="BED file"
+                       help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."/>
+            </when>
+        </conditional>
+        <expand macro="chain" />
+
+        <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers"
+               help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="output" label="${tool.name} on ${on_string}" />
+        <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
+    </outputs>
+
+    <tests>
+    <!-- BED -->
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+
+            <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
+        </test>
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
+            <param name="include_fails" value="True"/>
+
+            <output name="output" file="test_bed_01_output_a__all.bed"/>
+        </test>
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
+            <param name="include_fails" value="False"/>
+
+            <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
+        </test>
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
+            <param name="include_fails" value="True"/>
+
+            <output name="output" file="test_bed_02_output_a__all.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+BED
+---
+
+BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
+BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
+
+    A BED (Browser Extensible Data) file is a tab-delimited text file
+    describing genome regions or gene annotations. It is the standard file
+    format used by UCSC. It consists of one line per feature, each containing
+    3-12 columns. CrossMap converts BED files with less than 12 columns to a
+    different assembly by updating the chromosome and genome coordinates only;
+    all other columns remain unchanged. Regions from old assembly mapping to
+    multiple locations to the new assembly will be split. For 12-columns BED
+    files, all columns will be updated accordingly except the 4th column (name
+    of bed line), 5th column (score value) and 9th column (RGB value describing
+    the display color). 12-column BED files usually define multiple blocks (eg.
+    exon); if any of the exons fails to map to a new assembly, the whole BED
+    line is skipped.
+
+    NOTE:
+
+    1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
+       column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
+       any). All other columns will keep AS-IS.
+    2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
+    3. Lines will less than 3 columns will be skipped.
+    4. 2nd-column and 3-column must be integer, otherwise skipped.
+    5. “+” strand is assumed if no strand information was found.
+    6. For standard BED format (12 columns). If any of the defined exon blocks
+       cannot be uniquely mapped to target assembly, the whole entry will be
+       skipped.
+    7. If input region cannot be consecutively mapped target assembly, it will be split.
+    8. *.unmap file contains regions that cannot be unambiguously converted.
+
+Please see `the manual <http://crossmap.sourceforge.net/#convert-bed-format-files>`__ for more details.
+]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>