--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read_hexamer.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -0,0 +1,137 @@
+<tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@WRAPPER_VERSION@">
+    <description>
+        calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences
+    </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[read_hexamer.py --version]]></version_command>
+
+    <command><![CDATA[
+        #import re
+        #set $input_list = []
+        #for $i, $input in enumerate($inputs):
+
+            #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
+            #if $safename in $input_list:
+                #set $safename = str($safename) + "." + str($i)
+            #end if
+            $input_list.append($safename)
+
+            #if $input.is_of_type("fastq.gz", "fastqsanger.gz"):
+                gunzip -c '${input}' > "${safename}" &&
+            #else:
+                ln -sf '${input}' "${safename}" &&
+            #end if
+        #end for
+        read_hexamer.py -i '${ ','.join( [ $name for $name in $input_list ] ) }'
+        #if $refgenome:
+            -r '${refgenome}'
+        #end if
+        #if $refgene:
+            -g '${refgene}'
+        #end if
+        > '${output}'
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true" />
+        <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" />
+        <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" />
+                    <has_line line="AAAAAA&#009;0.00217391304348" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" />
+                    <has_line line="AAAAAA&#009;0.00217391304348" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" />
+                    <has_line line="AAAAAA&#009;0.00217391304348&#009;0.00534759358289" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" />
+                    <has_line line="AAAAAA&#009;0.00217391304348&#009;0.00217391304348" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Unable to test with collections at the moment (requires type="data_collection" on the input)
+        <test>
+            <param name="inputs">
+                <collection type="list">
+                    <element name="read_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq" />
+                    <element name="read_2" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq" />
+                </collection>
+            </param>
+            <output name="output" file="output.read_hexamer.2.txt" />
+        </test>
+        -->
+    </tests>
+
+    <help><![CDATA[
+read_hexamer.py
++++++++++++++++++++++
+
+Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency
+is also calculated for the reference genome. If ‘-g’ was provided, hexamer
+frequency is also calculated for the mRNA sequences.
+
+Inputs
+++++++++++++++
+
+Input reads file
+    Read sequences in fasta or fastq format.
+
+Reference Genome
+    Reference genome sequence in fasta format.
+
+Reference Gene
+    Reference mRNA sequences in fasta format.
+
+
+Outputs
+++++++++++++++
+
+Tabular file of hexamer frequences in for each input.
+
+@ABOUT@
+
+]]>
+    </help>
+
+    <expand macro="citations" />
+
+</tool>