Mercurial > repos > iuc > circos

changeset 3:fd59d783248a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f04fe62fb7dbad75e597da8cd674cfe36ed3d80a"
author iuc
date Mon, 02 Dec 2019 08:14:29 -0500
parents 014a21767ac4
children 184dfd9e113d
files circos.xml macros.xml tableviewer.xml
diffstat 3 files changed, 12 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/circos.xml	Tue Sep 17 16:54:57 2019 -0400
+++ b/circos.xml	Mon Dec 02 08:14:29 2019 -0500
@@ -62,13 +62,13 @@
     #end if
 #end if
 
-mv '$circos_conf' circos/conf/circos.conf &&
-mv '$ticks_conf' circos/conf/ticks.conf &&
-mv '$ideogram_conf' circos/conf/ideogram.conf &&
-mv '$data_conf'  circos/conf/data.conf &&
-mv '$highlight_conf'  circos/conf/highlight.conf &&
-mv '$links_conf'  circos/conf/links.conf &&
-mv '$test_case_conf' circos/conf/galaxy_test_case.json &&
+cp '$circos_conf' circos/conf/circos.conf &&
+cp '$ticks_conf' circos/conf/ticks.conf &&
+cp '$ideogram_conf' circos/conf/ideogram.conf &&
+cp '$data_conf'  circos/conf/data.conf &&
+cp '$highlight_conf'  circos/conf/highlight.conf &&
+cp '$links_conf'  circos/conf/links.conf &&
+cp '$test_case_conf' circos/conf/galaxy_test_case.json &&
 
 ## Highlights
 #for $hi, $data in enumerate($sec_highlight.data):
@@ -86,13 +86,11 @@
 #end for
 
 #if $outputs.tar == "yes"
-    tar cvfz circos.tar.gz circos >/dev/null
-#else
-    echo ''
+    tar -czf circos.tar.gz circos &&
 #end if
 
 #if $outputs.svg == "yes" or $outputs.png == "yes":
-    && circos -conf circos/conf/circos.conf -noparanoid
+    circos -conf circos/conf/circos.conf -noparanoid
 #end if
     ]]></command>
     <configfiles>
--- a/macros.xml	Tue Sep 17 16:54:57 2019 -0400
+++ b/macros.xml	Mon Dec 02 08:14:29 2019 -0500
@@ -2,7 +2,7 @@
 <macros>
   <token name="@CIRCOS_VERSION@">0.69.8</token>
 
-  <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy1</token>
+  <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy2</token>
 
   <xml name="requirements">
       <requirements>
@@ -12,6 +12,7 @@
         <requirement type="package" version="1.70">biopython</requirement>
         <requirement type="package" version="0.3.13">pybigwig</requirement>
         <requirement type="package" version="0.23">circos-tools</requirement>
+        <requirement type="package" version="1.29">tar</requirement>
         <yield />
       </requirements>
   </xml>
--- a/tableviewer.xml	Tue Sep 17 16:54:57 2019 -0400
+++ b/tableviewer.xml	Mon Dec 02 08:14:29 2019 -0500
@@ -14,7 +14,7 @@
 
 make-conf -dir circos/data < tmp &&
 
-tar cvfz circos.tar.gz circos &&
+tar -czf circos.tar.gz circos &&
 cd circos &&
 circos -conf etc/circos.conf &&
 mv circos.png ../ &&