# HG changeset patch
# User rnateam
# Date 1433766717 14400
# Node ID 8ebf2202a0d1dec471ab18fc201b016ec8cfb6a6
# Parent  eeedd1755f92ec0d0a5ea56be95ddf4f0fe5b2db
Uploaded

diff -r eeedd1755f92 -r 8ebf2202a0d1 compalignp.xml
--- a/compalignp.xml	Fri Jun 05 06:10:48 2015 -0400
+++ b/compalignp.xml	Mon Jun 08 08:31:57 2015 -0400
@@ -12,14 +12,12 @@
     compalignp
         -t $rna_alignment_target
         -r $rna_alignment_reference
-        $flag_verbose
     > $output
 ]]>
     </command>
     <inputs>
-        <param format="stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
-        <param format="stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
-        <param name="flag_verbose" type="boolean" truevalue="-v" falsevalue="" label="Verbose output" help="(-v)" />
+        <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)" />
     </inputs>
     <outputs>
         <data name="output" format="txt" />
diff -r eeedd1755f92 -r 8ebf2202a0d1 test-data/eukaryotic-trnas_2.1.clustal
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eukaryotic-trnas_2.1.clustal	Mon Jun 08 08:31:57 2015 -0400
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34      TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35      GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+                                     ************************************** ************** ******* ********* 
+
diff -r eeedd1755f92 -r 8ebf2202a0d1 test-data/eukaryotic-trnas_2.1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eukaryotic-trnas_2.1.out	Mon Jun 08 08:31:57 2015 -0400
@@ -0,0 +1,1 @@
+1.00
diff -r eeedd1755f92 -r 8ebf2202a0d1 tests/eukaryotic-trnas_2.1.clustal
--- a/tests/eukaryotic-trnas_2.1.clustal	Fri Jun 05 06:10:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-CLUSTAL 2.1 multiple sequence alignment
-
-
-Anolis_carolinensis_chrUn_GL34      TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
-Anolis_carolinensis_chrUn_GL35      GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
-                                     ************************************** ************** ******* ********* 
-
diff -r eeedd1755f92 -r 8ebf2202a0d1 tests/eukaryotic-trnas_2.1.out
--- a/tests/eukaryotic-trnas_2.1.out	Fri Jun 05 06:10:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-1.00
diff -r eeedd1755f92 -r 8ebf2202a0d1 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 05 06:10:48 2015 -0400
+++ b/tool_dependencies.xml	Mon Jun 08 08:31:57 2015 -0400
@@ -13,9 +13,14 @@
                     </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">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
+                <environment_variable action="set_to" name="COMPALIGNP_ROOT_PATH">$INSTALL_DIR/bin</environment_variable>
             </actions>
         </install>
     </package>