# HG changeset patch
# User iuc
# Date 1547245253 18000
# Node ID 8ca7e26aa959f6856ef33a9d2f349e2b110bcd34
# Parent 0919c78f7be8e34ae08a6d9801beafb7098854d3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
diff -r 0919c78f7be8 -r 8ca7e26aa959 gemini_macros.xml
--- a/gemini_macros.xml Mon Dec 17 12:20:06 2018 -0500
+++ b/gemini_macros.xml Fri Jan 11 17:20:53 2019 -0500
@@ -21,9 +21,17 @@
+
+
+
+ 10.1371/journal.pcbi.1003153
+
+
+
+
@@ -33,31 +41,36 @@
-
-
-
-
-
-
-
+
+
+
+
+
-
-
+
+
+
-
+
-
-
-
+
+
+
+
-
-
-
+
+
+
+
+
+
+
@@ -66,27 +79,23 @@
-
+
-
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
@@ -100,10 +109,90 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ value.strip()
+
+
+
+
+
+
+
+
+
+ value.strip()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ value.strip()
+
+
+ not value or value.isdigit()
+
+
+ not value or value.isdigit()
+
+
+
+
@@ -116,67 +205,50 @@
#end if
-
- #if str($filter.filter_selector) == 'yes' and $filter.filter:
- --filter '${ str( $filter.filter ) }'
+
+ #if str($report.report_selector) == 'full':
+ #set cols = "*"
+ #else:
+ #if $report.columns and str($report.columns) != '':
+ #set $cols = str($report.columns)
+ #else
+ #set $cols = ''
+ #end if
+ #if str($report.extra_cols).strip():
+ #if $cols:
+ #set $cols = $cols + ', ' + str($report.extra_cols)
+ #else:
+ #set $cols = str($report.extra_cols)
+ #end if
+ #end if
+ #if not $cols:
+ #set $cols = "variant_id, gene"
+ #end if
#end if
- #if $report.report_selector != 'all':
- --columns "${report.columns}
- #if str($report.extra_cols).strip()
- #echo ','+','.join(str($report.extra_cols).split())
- #end if
- "
+ @SET_COLS@
+ #if $cols != "*"
+ --columns '$cols'
#end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1371/journal.pcbi.1003153
-
-
-
-
-
-
-
-
-
- value is not None and value.metadata.gemini_version == "@VERSION@"
-
-
-
+ = %d" % int($r.start))
+ #end if
+ #if str($r.stop).strip():
+ #silent $r_elements.append("end <= %d" % int($r.stop))
+ #end if
+ #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
+ #end for
+ ]]>
+
diff -r 0919c78f7be8 -r 8ca7e26aa959 repository_dependencies.xml
--- a/repository_dependencies.xml Mon Dec 17 12:20:06 2018 -0500
+++ b/repository_dependencies.xml Fri Jan 11 17:20:53 2019 -0500
@@ -1,4 +1,4 @@
-
+
\ No newline at end of file