# HG changeset patch
# User iuc
# Date 1449092045 18000
# Node ID 8a1cd8a32a728c9b35909593ff06cdd555f050df
# Parent  ae7de35846d8c60a53313255adc20f8f6ba2e423
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit 746aa691891448484ef9f6417c708b6c7e8f60b0

diff -r ae7de35846d8 -r 8a1cd8a32a72 reprof.xml
--- a/reprof.xml	Wed Dec 02 15:14:28 2015 -0500
+++ b/reprof.xml	Wed Dec 02 16:34:05 2015 -0500
@@ -6,27 +6,51 @@
   </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" />
+      <param name="outputs" type="select" multiple="true" label="Additional Outputs">
+        <option value="pE">Probability of Extended/Sheet</option>
+        <option value="pH">Probability of Helix</option>
+        <option value="pL">Probability of Loop</option>
+        <option value="RI_S">Secondary Structure Reliability Index</option>
+
+        <option value="PACC">Absolute Solvent Accessibility</option>
+        <option value="PREL">Relative Solvent Accessibility</option>
+        <option value="P10">Relative Solvent Accessibility</option>
+        <option value="RI_A">Solvent Accessibility Reliability Index</option>
+      </param>
   </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 (${on_string})"/>
+      <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})">
+        <filter>'pE' in outputs</filter>
+      </data>
+      <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})">
+        <filter>'pH' in outputs</filter>
+      </data>
+      <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" >
+        <filter>'pL' in outputs</filter>
+      </data>
+      <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})">
+        <filter>'RI_S' in outputs</filter>
+      </data>
 
       <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})"/>
+      <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}">
+        <filter>'PACC' in outputs</filter>
+      </data>
+      <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}">
+        <filter>'PREL' in outputs</filter>
+      </data>
+      <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}">
+        <filter>'P10' in outputs</filter>
+      </data>
+      <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})">
+        <filter>'RI_A' in outputs</filter>
+      </data>
   </outputs>
   <tests>
       <test>
diff -r ae7de35846d8 -r 8a1cd8a32a72 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 02 15:14:28 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 02 16:34:05 2015 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="fann" version="2.2.0">
-        <repository changeset_revision="28d4ebb94540" name="package_fann_2_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0f570ce183a8" name="package_fann_2_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="perl_ai_fann" version="0.10">
-        <repository changeset_revision="11045607d36d" name="package_perl_ai_fann_0_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2e39b7570b10" name="package_perl_ai_fann_0_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="reprof" version="1.0.1">
-        <repository changeset_revision="a7ea224db803" name="package_reprof_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c98805a46c88" name="package_reprof_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>