# HG changeset patch # User erasmus-medical-center # Date 1487193321 18000 # Node ID 2c56a59a112f9d9ebb13b2afe79b4486a86b4c3f # Parent 10e2ea79ec55c4307bbb0a6c073733058742de4a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122 diff -r 10e2ea79ec55 -r 2c56a59a112f example.fa.1.bed --- a/example.fa.1.bed Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -chr1 0 330 diff -r 10e2ea79ec55 -r 2c56a59a112f example.fa.2.bed --- a/example.fa.2.bed Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -chr1 330 600 diff -r 10e2ea79ec55 -r 2c56a59a112f test-data/example.2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.2.vcf Wed Feb 15 16:15:21 2017 -0500 @@ -0,0 +1,26 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO== 15"> +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT== 15"> +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 +chr1 17 . TT T . PASS ADP=8;WT=0;HET=0;HOM=2;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:3:5 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:3:5 +chr1 77 . A AA . PASS ADP=8;WT=0;HET=0;HOM=2;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:0:8 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:0:8 diff -r 10e2ea79ec55 -r 2c56a59a112f test-data/example.fa.1.bed --- a/test-data/example.fa.1.bed Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -chr1 0 330 diff -r 10e2ea79ec55 -r 2c56a59a112f test-data/example.fa.2.bed --- a/test-data/example.fa.2.bed Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -chr1 330 600 diff -r 10e2ea79ec55 -r 2c56a59a112f test-data/example.fa.fai --- a/test-data/example.fa.fai Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -chr1 600 6 60 61 diff -r 10e2ea79ec55 -r 2c56a59a112f tool_dependencies.xml --- a/tool_dependencies.xml Thu Nov 05 10:00:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ - - - - - - - - - - - - - - diff -r 10e2ea79ec55 -r 2c56a59a112f varscan_mpileup2indel.xml --- a/varscan_mpileup2indel.xml Thu Nov 05 10:00:19 2015 -0500 +++ b/varscan_mpileup2indel.xml Wed Feb 15 16:15:21 2017 -0500 @@ -1,41 +1,39 @@ - - VarScan2 INDEL detection; directly from a *.mpileup file. + + VarScan2 INDEL detection (on mpileup data) - varscan + varscan - java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1 + varscan 2>&1 | head -n 1 - - cat $mpileup_input | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - mpileup2indel - - #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 - > $snv_output ; - cat stderr.txt - + '${snv_output}' + ]]> - + @@ -45,12 +43,12 @@ - - - - - - + + + + + + @@ -81,51 +79,21 @@ -**VarScan 2.3.6** +**VarScan 2.4.2** 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. http://dx.doi.org/10.1101/gr.129684.111 http://www.ncbi.nlm.nih.gov/pubmed/19542151 -*VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. -The samtools package is not able to parallelize the mpileup generation which make it a very slow process. -Other people were aware of this and have written a version that can do parallelization: -https://github.com/mydatascience/parallel-mpileup - -Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan. - -.. _VarScan: http://varscan.sourceforge.net/ - **Input formats** -VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. +Alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. **Installation** Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. - -**License** - -* VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) -* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING) - -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.g2.bx.psu.edu/ - -http://testtoolshed.g2.bx.psu.edu/ 10.1101/gr.129684.111 - \ No newline at end of file + diff -r 10e2ea79ec55 -r 2c56a59a112f varscan_mpileup2indel_from_bam.xml --- a/varscan_mpileup2indel_from_bam.xml Thu Nov 05 10:00:19 2015 -0500 +++ b/varscan_mpileup2indel_from_bam.xml Wed Feb 15 16:15:21 2017 -0500 @@ -1,126 +1,97 @@ - + VarScan2 INDEL 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 + varscan + sambamba - java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1 + varscan 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 $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 - #else - #import os.path + - #if not os.path.isfile(str($alignment)+".bai") - echo "- Indexing alignment file: $alignment.name " ; - samtools index $alignment 2>&1 ; - #else - echo "- Skiping indexing: $alignment.name " ; - #end if + '${alignment}' #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 + --samtools + -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.sambamba_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 - #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 -k1,1V -k2,2g - #end if - #end if - - | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - mpileup2indel - - #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 INDEL detect ]-------------" ; - cat stderr_2.txt ; - echo "" ; - echo "----------------------------------------------------" ; + -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 + + | varscan mpileup2indel + + #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 $varscan_output.value == "vcf" + --output-vcf 1 + #end if + + > '${snv_output}' + + ]]> @@ -179,18 +150,6 @@ - - - - - - - - - - - - @@ -260,30 +219,12 @@ - - - - - - - - - - - - - - - - - - - + -**VarScan 2.3.6** +**VarScan 2.4.2** 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. http://dx.doi.org/10.1101/gr.129684.111 @@ -302,33 +243,18 @@ VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. -**Installation** - -Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. - **License** -* VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) -* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING) +* VarScan 2.4.2: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) Contact ------- The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.g2.bx.psu.edu/ - -http://testtoolshed.g2.bx.psu.edu/ +Medical Center (Rotterdam, Netherlands). 10.1101/gr.129684.111 - \ No newline at end of file +