# HG changeset patch
# User devteam
# Date 1484758049 18000
# Node ID 3213c223678c390fbedc95462d4ff365679c6ac8
# Parent 29ba2103739c4a3f1e8e6809dff0ac027cd8540f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
diff -r 29ba2103739c -r 3213c223678c bamtools-filter.xml
--- a/bamtools-filter.xml Fri Jan 13 11:02:24 2017 -0500
+++ b/bamtools-filter.xml Wed Jan 18 11:47:29 2017 -0500
@@ -1,215 +1,212 @@
-
- BAM datasets on a variety of attributes
-
- bamtools
-
-
- cat $script_file > $out_file2;
-
- #for $bam_count, $input_bam in enumerate( $input_bams ):
- ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
- ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
- #end for
-
- bamtools
- filter
- -script $script_file
-
- #for $bam_count, $input_bam in enumerate( $input_bams ):
- -in "localbam_${bam_count}.bam"
- #end for
- -out $out_file1
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+
+ BAM datasets on a variety of attributes
+
+ bamtools
+
+
+ $out_file2;
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
+ ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+ #end for
+ bamtools
+ filter
+ -script $script_file
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ -in "localbam_${bam_count}.bam"
+ #end for
+ -out $out_file1
+ ]]>
+
+
+
+ ##Sets up a json configfile for bamtools filter
+ ##If there is more than one condition prints brackets and "filters:"
+ #if len( $conditions ) > 1
+ {
+ "filters":
+ [
+ #end if
+ #for $i, $c in enumerate( $conditions, start=1 )
+ { "id": "$i",
+ #for $j, $s in enumerate( $c.filters, start=1 )
+ ##The if below takes care of the comma at the end of last condition within group
+ #if $j != len( $c.filters)
+ "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
+ #else
+ "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
+ #end if
+ #end for
+ ##The if below takes care of the comma at the end of last condition within group
+ #if $i != len( $conditions )
+ },
+ #else
+ }
+ #end if
+ #end for
+ #if len( $conditions ) > 1
+ #if str( $rule_configuration.rules_selector ) == "True":
+ ],
+ "rule" : "${rule_configuration.rules}"
+ #else
+ ]
+ #end if
+ }
+ #end if
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- ##Sets up a json configfile for bamtools filter
- ##If there is more than one condition prints brackets and "filters:"
- #if len( $conditions ) > 1
- {
- "filters":
- [
- #end if
- #for $i, $c in enumerate( $conditions, start=1 )
- { "id": "$i",
- #for $j, $s in enumerate( $c.filters, start=1 )
- ##The if below takes care of the comma at the end of last condition within group
- #if $j != len( $c.filters)
- "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
- #else
- "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
- #end if
- #end for
- ##The if below takes care of the comma at the end of last condition within group
- #if $i != len( $conditions )
- },
- #else
- }
- #end if
- #end for
- #if len( $conditions ) > 1
- #if str( $rule_configuration.rules_selector ) == "True":
- ],
- "rule" : "${rule_configuration.rules}"
- #else
- ]
- #end if
- }
- #end if
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@@ -218,7 +215,7 @@
-
+
**What is does**
BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
@@ -318,8 +315,8 @@
Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
- 10.1093/bioinformatics/btr174
-
+
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+ 10.1093/bioinformatics/btr174
+
diff -r 29ba2103739c -r 3213c223678c tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jan 13 11:02:24 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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