--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat May 06 13:18:09 2017 -0400
@@ -0,0 +1,65 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <token name="@WRAPPER_VERSION@">0.14</token>
+    <xml name="requirements_stdio">
+        <requirements>
+            <requirement type="package" version="0.1.19">samtools</requirement>
+            <yield/>
+        </requirements>
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+        <version_command>bismark --version</version_command>
+    </xml>
+
+    <xml name="single_paired_conditional">
+        <!-- Input Parameters -->
+        <conditional name="singlePaired">
+            <param name="sPaired" type="select" label="Is this library mate-paired?">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
+            </when>
+            <when value="paired">
+                <repeat name="mate_list" title="Paired End Pairs" min="1">
+                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
+                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
+                </repeat>
+                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
+                <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="advanced_params">
+        <param name="seed_len" type="integer" value="28" label="Seed length"
+            help="The number of bases of the high quality end of the read to which the maximum number of mismatches applies. (--seed-len)" />
+        <param name="qupto" type="integer" value="0" min="0" label="Only aligns the first N reads or read pairs from the input"
+            help="Default is 0 and means 'no-limit'. (--qupto)"/>
+        <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input"
+            help="(--skip-reads)" />
+
+        <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
+            label="Write ambiguous reads to an extra output file"
+            help="Write all reads which produce more than one valid alignment with the same number of lowest
+                mismatches or other reads that fail to align uniquely. (--output-suppressed-reads-r/l)" />
+        <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
+            label="Write all reads that could not be aligned to a file. (--output-unmapped-reads-r/l)" />
+
+        <!-- output Options -->
+        <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
+        <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
+        <!--end output options -->
+
+    </xml>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr167</citation>
+        </citations>
+    </xml>
+</macros>