changeset 1:31a354009216 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f

--- a/reago.xml	Tue Jan 26 08:17:20 2016 -0500
+++ b/reago.xml	Thu Feb 02 19:35:52 2017 -0500
@@ -1,9 +1,7 @@
-<tool id="reago" name="Reago" version="0.1.0">
+<tool id="reago" name="Reago" version="1.1">
     <description> to assemble rRNA</description>
 
     <requirements>
-        <requirement type="package" version="1.1">infernal</requirement>
-        <requirement type="package" version="1.5.7">genometools</requirement>
         <requirement type="package" version="1.1">reago</requirement>
     </requirements>
 
@@ -23,16 +21,16 @@
             --r2_output $r2_output
 
         &&  
-        python \${REAGO_DIR}/filter_input.py 
+        filter_input.py 
             $r1_output
             $r2_output
             .
-            \${REAGO_DIR}/cm/ 
+            \$(dirname \$(which reago.py))/cm/ 
             $cm_to_use
             "\${GALAXY_SLOTS:-4}"
 
         && 
-        python \${REAGO_DIR}/reago.py 
+        reago.py 
             "filtered.fasta"
             .
             -l $read_length
@@ -135,4 +133,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv231</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>

Binary file release-2015.12.18.tar.gz has changed

--- a/tool_dependencies.xml	Tue Jan 26 08:17:20 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="infernal" version="1.1">
-        <repository changeset_revision="bd0a14c43fc2" name="package_infernal_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="genometools" version="1.5.7">
-        <repository changeset_revision="e89d0691dcda" name="package_genometools_1_5_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="reago" version="1.1">
-        <install version="1.0">
-            <actions>
-                <action sha256sum="585e21cd9edf0f7a60c758230ab2faf9948ad1b8b16089e283b6cb2df2e10626" type="download_by_url">https://github.com/chengyuan/reago-1.1/archive/release-2015.12.18.tar.gz</action>
-                <action type="move_file">
-                    <source>reago.py</source>
-                    <destination>$INSTALL_DIR/</destination>
-                </action>
-                <action type="move_file">
-                    <source>filter_input.py</source>
-                    <destination>$INSTALL_DIR/</destination>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>cm</source_directory>
-                    <destination_directory>$INSTALL_DIR/cm/</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="REAGO_DIR">$INSTALL_DIR/</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
-</tool_dependency>