# HG changeset patch
# User yhoogstrate
# Date 1446714849 18000
# Node ID f7798cd80cf555175d9fff2466d71f2479cba997
# Parent c1424388f08b02ca8b9376dd1bde7cfb829b2a5f
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
diff -r c1424388f08b -r f7798cd80cf5 samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml Thu Nov 05 03:45:02 2015 -0500
+++ b/samtools-parallel-mpileup.xml Thu Nov 05 04:14:09 2015 -0500
@@ -1,218 +1,221 @@
- Samtools mpileup (supporting parallelization)
-
- ncurses
- samtools_parallel_mpileup_0_1_19a
- package_samtools_0_1_19
-
-
- #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
- echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
- #else
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- samtools-parallel-mpileup mpileup
- -t $mpileup_parallelization.samtools_threads
- #else
- samtools mpileup
- #end if
- -f
- #if $reference_genome_source.source_select == "indexed_filtered"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "indexed_all"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "history"
- "$reference_genome_source.reference_genome"
- #else
-
- "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
- #end if
-
- #if $extended_parameters_regions.samtools_regions == "region"
- -r $extended_parameters_regions.$samtools_r
- #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
- -l $extended_parameters_regions.$samtools_l
- #end if
-
- #if $extended_parameters.parameters == "extended"
- $extended_parameters.samtools_6
- $extended_parameters.samtools_A
- $extended_parameters.samtools_B
- -C $extended_parameters.samtools_C
- -d $extended_parameters.samtools_d
- $extended_parameters.samtools_E
- -M $extended_parameters.samtools_M
- $extended_parameters.samtools_R
- -q $extended_parameters.samtools_q
- -Q $extended_parameters.samtools_Q
-
- -e $extended_parameters.samtools_e
- -F $extended_parameters.samtools_F
- -h $extended_parameters.samtools_h
- $extended_parameters.samtools_I
- -L $extended_parameters.samtools_L
- -m $extended_parameters.samtools_m
- -o $extended_parameters.samtools_o
- $extended_parameters.samtools_p
- -P $extended_parameters.samtools_P
- #end if
-
- #for $alignment in $alignments
- ${alignment}
- #end for
-
- 2> stderr_1.txt
-
- #if $sort_mpileup
- | sort -k 1,1 -k 2,2
- #end if
-
- > $output ;
- cat stderr_1.txt
- #end if
-
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+ Samtools mpileup (supporting parallelization)
+
+
+ samtools_parallel_mpileup_0_1_19a
+ package_samtools_0_1_19
+
+
+ samtools --version | head -n 1 | awk '{ print $2 }'
+
+
+ #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
+ echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
+ #else
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ samtools-parallel-mpileup mpileup
+ -t $mpileup_parallelization.samtools_threads
+ #else
+ samtools mpileup
+ #end if
+ -f
+ #if $reference_genome_source.source_select == "indexed_filtered"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "indexed_all"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "history"
+ "$reference_genome_source.reference_genome"
+ #else
+
+ "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ #end if
+
+ #if $extended_parameters_regions.samtools_regions == "region"
+ -r $extended_parameters_regions.$samtools_r
+ #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
+ -l $extended_parameters_regions.$samtools_l
+ #end if
+
+ #if $extended_parameters.parameters == "extended"
+ $extended_parameters.samtools_6
+ $extended_parameters.samtools_A
+ $extended_parameters.samtools_B
+ -C $extended_parameters.samtools_C
+ -d $extended_parameters.samtools_d
+ $extended_parameters.samtools_E
+ -M $extended_parameters.samtools_M
+ $extended_parameters.samtools_R
+ -q $extended_parameters.samtools_q
+ -Q $extended_parameters.samtools_Q
+
+ -e $extended_parameters.samtools_e
+ -F $extended_parameters.samtools_F
+ -h $extended_parameters.samtools_h
+ $extended_parameters.samtools_I
+ -L $extended_parameters.samtools_L
+ -m $extended_parameters.samtools_m
+ -o $extended_parameters.samtools_o
+ $extended_parameters.samtools_p
+ -P $extended_parameters.samtools_P
+ #end if
+
+ #for $alignment in $alignments
+ ${alignment}
+ #end for
+
+ 2> stderr_1.txt
+
+ #if $sort_mpileup
+ | sort -k 1,1 -k 2,2
+ #end if
+
+ > $output ;
+ cat stderr_1.txt
+ #end if
+
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**Samtools mpileup (supporting parallelization)**
@@ -268,12 +271,24 @@
http://testtoolshed.g2.bx.psu.edu/
-
- @unpublished{samtools_parallel_mpileup,
- author = {Youri Hoogstrate},
- title = { Samtools parallel-mpileup, fork of classical samtools },
- year = 2014,
- url = { https://github.com/yhoogstrate/parallel-mpileup }
- }
-
+
+
+ @unpublished{samtools_parallel_mpileup,
+ author = {Youri Hoogstrate},
+ title = { Samtools parallel-mpileup, fork of classical samtools },
+ year = 2014,
+ url = { https://github.com/yhoogstrate/parallel-mpileup }
+ }
+
+
+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+
+
+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
+
+
\ No newline at end of file
diff -r c1424388f08b -r f7798cd80cf5 varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml Thu Nov 05 03:45:02 2015 -0500
+++ b/varscan_mpileup2snp.xml Thu Nov 05 04:14:09 2015 -0500
@@ -1,85 +1,86 @@
- VarScan2 SNP/SNV detection; directly from a *.mpileup file.
-
- varscan
-
-
- java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1
-
-
- cat $mpileup_input | java
- -Xmx64G
- -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
- mpileup2snp
-
- #if $extended_parameters.parameters == "extended"
- --min-coverage $extended_parameters.varscan_min_coverage
- --min-reads2 $extended_parameters.varscan_min_reads2
- --min-avg-qual $extended_parameters.varscan_min_avg_qual
- --min-var-freq $extended_parameters.varscan_min_var_freq
- --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
- --p-value $extended_parameters.varscan_p_value
- $extended_parameters.varscan_strand_filter
- $extended_parameters.varscan_variants
- #end if
-
- #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
- --output-vcf 1
- #end if
-
- 2> stderr.txt
- > $snv_output ;
- cat stderr.txt
-
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+ VarScan2 SNP/SNV detection; directly from a *.mpileup file.
+
+
+ varscan
+
+
+ java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1
+
+
+ cat $mpileup_input | java
+ -Xmx64G
+ -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
+ mpileup2snp
+
+ #if $extended_parameters.parameters == "extended"
+ --min-coverage $extended_parameters.varscan_min_coverage
+ --min-reads2 $extended_parameters.varscan_min_reads2
+ --min-avg-qual $extended_parameters.varscan_min_avg_qual
+ --min-var-freq $extended_parameters.varscan_min_var_freq
+ --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+ --p-value $extended_parameters.varscan_p_value
+ $extended_parameters.varscan_strand_filter
+ $extended_parameters.varscan_variants
+ #end if
+
+ #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
+ --output-vcf 1
+ #end if
+
+ 2> stderr.txt
+ > $snv_output ;
+ cat stderr.txt
+
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**VarScan 2.3.6**
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
diff -r c1424388f08b -r f7798cd80cf5 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml Thu Nov 05 03:45:02 2015 -0500
+++ b/varscan_mpileup2snp_from_bam.xml Thu Nov 05 04:14:09 2015 -0500
@@ -1,282 +1,285 @@
- VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.
-
- samtools_parallel_mpileup_0_1_19a
- samtools
- varscan
- ncurses
-
-
- #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
- echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
- #else
- #import os.path
- #for $alignment in $alignments
-
- #if not os.path.isfile(str($alignment)+".bai")
- echo "- Indexing alignment file: $alignment.name " ;
- samtools index $alignment 2>&1 ;
- #else
- echo "- Skiping indexing: $alignment.name " ;
- #end if
- #end for
-
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- samtools-parallel-mpileup mpileup
- -t $mpileup_parallelization.samtools_threads
- #else
- samtools mpileup
- #end if
- -f
- #if $reference_genome_source.source_select == "indexed_filtered"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "indexed_all"
- "$reference_genome_source.reference_genome"
- #else if $reference_genome_source.source_select == "history"
- "$reference_genome_source.reference_genome"
- #else
-
- "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
- #end if
-
- #if $extended_parameters_regions.samtools_regions == "region"
- -r $extended_parameters_regions.samtools_r
- #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
- -l $extended_parameters_regions.samtools_l
- #end if
-
- #if $extended_parameters.parameters == "extended"
- $extended_parameters.samtools_6
- $extended_parameters.samtools_A
- $extended_parameters.samtools_B
- -C $extended_parameters.samtools_C
- -d $extended_parameters.samtools_d
- $extended_parameters.samtools_E
- -M $extended_parameters.samtools_M
- $extended_parameters.samtools_R
- -q $extended_parameters.samtools_q
- -Q $extended_parameters.samtools_Q
-
- -e $extended_parameters.samtools_e
- -F $extended_parameters.samtools_F
- -h $extended_parameters.samtools_h
- $extended_parameters.samtools_I
- -L $extended_parameters.samtools_L
- -m $extended_parameters.samtools_m
- -o $extended_parameters.samtools_o
- $extended_parameters.samtools_p
- -P $extended_parameters.samtools_P
- #end if
-
- #for $alignment in $alignments
- ${alignment}
- #end for
- 2>stderr_1.txt
-
- #if $mpileup_parallelization.mpileup_parallelization_select == "true"
- #if $mpileup_parallelization.sort_mpileup
- | sort -k 1,1 -k 2,2
- #end if
- #end if
-
- ## Make for every MPILEUP file an
- ## http://en.wikipedia.org/wiki/Named_pipe
-
- | java
- -Xmx64G
- -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
- mpileup2snp
-
- #if $extended_parameters.parameters == "extended"
- --min-coverage $extended_parameters.varscan_min_coverage
- --min-reads2 $extended_parameters.varscan_min_reads2
- --min-avg-qual $extended_parameters.varscan_min_avg_qual
- --min-var-freq $extended_parameters.varscan_min_var_freq
- --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
- --p-value $extended_parameters.varscan_p_value
- $extended_parameters.varscan_strand_filter
- $extended_parameters.varscan_variants
- #end if
-
- #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
- --output-vcf 1
- #end if
-
- 2>stderr_2.txt
- > $snv_output ;
-
-
- echo "---------------[ mpileup generation ]---------------" ;
- cat stderr_1.txt ;
- echo "" ;
- echo "---------------[ VarScan SNP detect ]---------------" ;
- cat stderr_2.txt ;
- echo "" ;
- echo "----------------------------------------------------" ;
- #end if
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+ VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.
+
+
+ samtools_parallel_mpileup_0_1_19a
+ samtools
+ varscan
+
+
+ java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1
+
+
+ #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
+ echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
+ #else
+ #import os.path
+ #for $alignment in $alignments
+
+ #if not os.path.isfile(str($alignment)+".bai")
+ echo "- Indexing alignment file: $alignment.name " ;
+ samtools index $alignment 2>&1 ;
+ #else
+ echo "- Skiping indexing: $alignment.name " ;
+ #end if
+ #end for
+
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ samtools-parallel-mpileup mpileup
+ -t $mpileup_parallelization.samtools_threads
+ #else
+ samtools mpileup
+ #end if
+ -f
+ #if $reference_genome_source.source_select == "indexed_filtered"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "indexed_all"
+ "$reference_genome_source.reference_genome"
+ #else if $reference_genome_source.source_select == "history"
+ "$reference_genome_source.reference_genome"
+ #else
+
+ "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ #end if
+
+ #if $extended_parameters_regions.samtools_regions == "region"
+ -r $extended_parameters_regions.samtools_r
+ #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
+ -l $extended_parameters_regions.samtools_l
+ #end if
+
+ #if $extended_parameters.parameters == "extended"
+ $extended_parameters.samtools_6
+ $extended_parameters.samtools_A
+ $extended_parameters.samtools_B
+ -C $extended_parameters.samtools_C
+ -d $extended_parameters.samtools_d
+ $extended_parameters.samtools_E
+ -M $extended_parameters.samtools_M
+ $extended_parameters.samtools_R
+ -q $extended_parameters.samtools_q
+ -Q $extended_parameters.samtools_Q
+
+ -e $extended_parameters.samtools_e
+ -F $extended_parameters.samtools_F
+ -h $extended_parameters.samtools_h
+ $extended_parameters.samtools_I
+ -L $extended_parameters.samtools_L
+ -m $extended_parameters.samtools_m
+ -o $extended_parameters.samtools_o
+ $extended_parameters.samtools_p
+ -P $extended_parameters.samtools_P
+ #end if
+
+ #for $alignment in $alignments
+ ${alignment}
+ #end for
+ 2>stderr_1.txt
+
+ #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+ #if $mpileup_parallelization.sort_mpileup
+ | sort -k 1,1 -k 2,2
+ #end if
+ #end if
+
+ ## Make for every MPILEUP file an
+ ## http://en.wikipedia.org/wiki/Named_pipe
+
+ | java
+ -Xmx64G
+ -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
+ mpileup2snp
+
+ #if $extended_parameters.parameters == "extended"
+ --min-coverage $extended_parameters.varscan_min_coverage
+ --min-reads2 $extended_parameters.varscan_min_reads2
+ --min-avg-qual $extended_parameters.varscan_min_avg_qual
+ --min-var-freq $extended_parameters.varscan_min_var_freq
+ --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+ --p-value $extended_parameters.varscan_p_value
+ $extended_parameters.varscan_strand_filter
+ $extended_parameters.varscan_variants
+ #end if
+
+ #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
+ --output-vcf 1
+ #end if
+
+ 2>stderr_2.txt
+ > $snv_output ;
+
+
+ echo "---------------[ mpileup generation ]---------------" ;
+ cat stderr_1.txt ;
+ echo "" ;
+ echo "---------------[ VarScan SNP detect ]---------------" ;
+ cat stderr_2.txt ;
+ echo "" ;
+ echo "----------------------------------------------------" ;
+ #end if
+
+
+
+
+
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**VarScan 2.3.6**
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.