--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_macros.xml	Wed May 30 15:36:08 2018 -0400
@@ -0,0 +1,58 @@
+<macros>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btu138</citation>
+            <yield />
+        </citations>
+    </xml>
+    
+    <xml name="requirements">
+        <requirements>
+              <requirement type="package" version="0.5.4">presto</requirement>
+        </requirements>
+    </xml>
+    
+    <xml name="presto-coord-param">
+        <param argument="--coord" type="select"  value="presto"  label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
+            <option value="illumina">Illumina</option>
+            <option value="solexa">Solexa</option>
+            <option value="sra">SRA</option>
+            <option value="454">454</option>
+            <option value="presto">pRESTO</option>
+        </param>
+    </xml>
+    
+    <xml name="presto-log-param">
+        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
+    </xml>
+    
+    <xml name="presto-log-output">
+        <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}">
+            <filter>capture_log</filter>
+        </data>
+    </xml>
+    
+    <xml name="text-regex-validator">
+        <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>
+    </xml>
+
+    <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io/en/latest/tools</token>
+    
+    <!-- When modifying this file ensure that the version here matches the version above in requirements. -->
+    <token name="@PRESTO_VERSION@">0.5.4</token>
+    
+    <token name="@HELP_NOTE@"><![CDATA[
+
+====
+
+**Note about limitations of pRESTO tools within Galaxy:**
+
+pRESTO tools in galaxy have the following limitations vs. when run at the command line:
+
+* Inputs must be FASTQ format and cannot be FASTA format.
+* Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
+    - Steps that take a pair of fastq inputs can only take two files, not two sets of files
+    - Steps that take a single set of fastq inputs can only take a single file
+* The ``--outdir`` and ``--outname`` options are not supported; output files are named directly
+    ]]></token>
+</macros>
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