--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reprof.xml	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool id="rost_reprof" name="reprof" version="@WRAPPER_VERSION@">
+  <description>protein secondary structure and accessibility prediction</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+      ##if str($query.ext) == 'pssm':
+      ##end if
+
+      ln -s $query query.fa;
+      python $__tool_directory__/reprof.py query.fa $REPROF_MODEL_DIR
+]]></command>
+  <inputs>
+      <param name="query" label="Protein sequences" type="data" format="fasta" />
+  </inputs>
+  <outputs>
+      <data format="gff3" name="secondary_structure" from_work_dir="secondary_structure.gff3" label="Secondary Structure of ${on_string}"/>
+      <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})"/>
+      <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})" />
+      <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" />
+      <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})"/>
+
+      <data format="gff3" name="solvent_accessibility" from_work_dir="solvent_accessibility.gff3" label="Solvent Accessibile Regions of ${on_string}" />
+      <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}"/>
+      <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}"/>
+      <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}"/>
+      <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="query" value="test.fa" />
+
+          <output name="secondary_structure" file="secondary_structure.gff3" />
+          <output name="solvent_accessibility" file="solvent_accessibility.gff3" />
+          <output name="pE" file="pE.wig" />
+          <output name="pH" file="pH.wig" />
+          <output name="pL" file="pL.wig" />
+          <output name="RI_S" file="RI_S.wig" />
+          <output name="PACC" file="PACC.wig" />
+          <output name="PREL" file="PREL.wig" />
+          <output name="P10" file="P10.wig" />
+          <output name="RI_A" file="RI_A.wig" />
+      </test>
+  </tests>
+  <help><![CDATA[
+reprof
+======
+
+Reprof is a protein secondary structure and accessibility predictor from the
+Rost Lab. Prediction is done from protein sequences.
+
+Three states of secondary structure are predicted: helix (H; includes alpha-,
+pi- and 3_10-helix), (beta-)strand (E = extended strand in beta-sheet
+conformation of at least two residues length) and loop (L).
+      ]]></help>
+  <citations>
+    <citation type="doi">10.1186/1471-2105-10-S13-O3</citation>
+    <citation type="doi">10.1002/pro.5560050824View</citation>
+  </citations>
+</tool>