# HG changeset patch
# User rnateam
# Date 1510485042 18000
# Node ID f3a318881b1b1c20be8dad28b1efeaa2f22ded1f
# Parent  7e55ac3bd4585882f3f853986f80407d167e39ed
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867

diff -r 7e55ac3bd458 -r f3a318881b1b compalignp.xml
--- a/compalignp.xml	Tue Jun 09 05:36:03 2015 -0400
+++ b/compalignp.xml	Sun Nov 12 06:10:42 2017 -0500
@@ -3,21 +3,17 @@
     <requirements>
         <requirement type="package" version="1.0">compalignp</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    </stdio>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
     compalignp
-        -t $rna_alignment_target
-        -r $rna_alignment_reference
+        -t '$rna_alignment_target'
+        -r '$rna_alignment_reference'
     > $output
 ]]>
     </command>
     <inputs>
-        <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
-        <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
+        <param format="clustal,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
+        <param format="clustal,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
     </inputs>
     <outputs>
         <data name="output" format="txt" />
@@ -31,6 +27,7 @@
     </tests>
     <help>
 <![CDATA[
+
 **compalignp**
 
 > Paranoia version of squids compalign. 
@@ -43,6 +40,6 @@
 ]]>
     </help>
 <citations>
-  <citation type="doi">10.1186/1748-7188-1-19</citation>
+    <citation type="doi">10.1186/1748-7188-1-19</citation>
 </citations>
 </tool>
diff -r 7e55ac3bd458 -r f3a318881b1b tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 09 05:36:03 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="squid" version="1.9g">
-        <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="compalignp" version="1.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.biophys.uni-duesseldorf.de/bralibase/compalignp.tgz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="squid" version="1.9g" />
-                    </repository>
-                </action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>compalignp</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="COMPALIGNP_ROOT_PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
-</tool_dependency>