# HG changeset patch
# User devteam
# Date 1484758031 18000
# Node ID 04866f817daaa250fbbf5287aca6c8863c1cd69e
# Parent ea3fc1adee7569ed0bb565bae49ef45d43668c05
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
diff -r ea3fc1adee75 -r 04866f817daa bamtools.xml
--- a/bamtools.xml Wed Nov 11 12:33:26 2015 -0500
+++ b/bamtools.xml Wed Jan 18 11:47:11 2017 -0500
@@ -1,232 +1,193 @@
-
- BAM datasets and perform other transformations
-
- bamtools
- samtools
-
-
-
- ##set up input files
-
- #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
-
- #if str( $analysis_type.analysis_type_selector ) == "convert":
- #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
- #set $reference_fasta_filename = "localref.fa"
- #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
- ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
- samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
- #else:
- #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
- #end if
- #end if
- #end if
-
- ##finished setting up inputs
-
- ##start bamtools commandline
-
- bamtools
-
- #if str( $analysis_type.analysis_type_selector ) == "convert":
-
- convert
-
- -format ${analysis_type.format_type.format_type_selector}
-
- #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
-
- ${analysis_type.format_type.mapqual}
- -fasta "${reference_fasta_filename}"
-
- #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
-
- ${analysis_type.format_type.noheader}
-
- #end if
-
- -out $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "count":
-
- count
- > $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "coverage":
-
- coverage
- -out $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "header":
-
- header
- > $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "merge":
-
- merge
- -out $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "random":
-
- random
- -n ${analysis_type.count}
- -seed ${analysis_type.seed}
- -out $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "revert":
-
- revert
- ${analysis_type.keepDuplicate}
- ${analysis_type.keepQualities}
- -out $out_file1
-
- #elif str( $analysis_type.analysis_type_selector ) == "sort":
-
- sort
- ${analysis_type.byname}
- -out $out_file1
-
- #end if
-
- #for $bam_count, $input_bam in enumerate( $input_bams ):
- -in "localbam_${bam_count}.bam"
- #end for
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+ BAM datasets and perform other transformations
+
+ bamtools
+ samtools
+
+
+
+
+
+ &1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
+ #else:
+ #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
+ #end if
+ #end if
+ #end if
+ bamtools
+ #if str( $analysis_type.analysis_type_selector ) == "convert":
+ convert
+ -format ${analysis_type.format_type.format_type_selector}
+ #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+ ${analysis_type.format_type.mapqual}
+ -fasta "${reference_fasta_filename}"
+ #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
+ ${analysis_type.format_type.noheader}
+ #end if
+ -out $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "count":
+ count
+ > $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "coverage":
+ coverage
+ -out $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "header":
+ header
+ > $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "merge":
+ merge
+ -out $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "random":
+ random
+ -n ${analysis_type.count}
+ -seed ${analysis_type.seed}
+ -out $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "revert":
+ revert
+ ${analysis_type.keepDuplicate}
+ ${analysis_type.keepQualities}
+ -out $out_file1
+ #elif str( $analysis_type.analysis_type_selector ) == "sort":
+ sort
+ ${analysis_type.byname}
+ -out $out_file1
+ #end if
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ -in "localbam_${bam_count}.bam"
+ #end for
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
+
**What is does**
@@ -284,8 +245,8 @@
Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
-
-
- 10.1093/bioinformatics/btr174
-
+
+
+ 10.1093/bioinformatics/btr174
+
diff -r ea3fc1adee75 -r 04866f817daa tool_dependencies.xml
--- a/tool_dependencies.xml Wed Nov 11 12:33:26 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-
-
-
-
-
-
-