# HG changeset patch # User iuc # Date 1489272887 18000 # Node ID 788510a3597ae41d2043c2f479dfed5dd27aac6b # Parent 45bbee2107932e1955a9140a0cd09962860f1e1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 diff -r 45bbee210793 -r 788510a3597a README.md --- a/README.md Tue Jan 31 12:39:05 2017 -0500 +++ b/README.md Sat Mar 11 17:54:47 2017 -0500 @@ -3,7 +3,7 @@ Copied from branch bcftools1.2: This aims to be a "faithful" rendering of the bcftool suite. I.e. options are -presented essentially as closely to the command line version as is useful. +presented essentially as closely to the command line version as is useful. This may not appeal to all, if you'd like to see smaller and more dedicated tools (e.g. "intersect", "union" and "complement" being separate tools instead @@ -11,12 +11,12 @@ Updated for bcftools v1.3 -This was extended from the bcftools1.2 branch then greatly hand edited to +This was extended from the bcftools1.2 branch then greatly hand edited to group params and manage param innteractions. -In the macros.xml there are macros and tokens to handle file input and output. +In the macros.xml there are macros and tokens to handle file input and output. These use the datatypes currently available in galaxy: Vcf and Bcf -The macros take care of bgzip and indexing of inputs. +The macros take care of bgzip and indexing of inputs. The convert command was split into 2 tools, "convert to vcf" and "convert from vcf" @@ -27,7 +27,7 @@ - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf - roh needs a more useful input.vcf for testing - plugin color chrs -- plugin frameshifts +- plugin frameshifts ## Status diff -r 45bbee210793 -r 788510a3597a bcftools_plugin_setgt.xml --- a/bcftools_plugin_setgt.xml Tue Jan 31 12:39:05 2017 -0500 +++ b/bcftools_plugin_setgt.xml Sat Mar 11 17:54:47 2017 -0500 @@ -1,5 +1,5 @@ - + plugin Sets genotypes setGT diff -r 45bbee210793 -r 788510a3597a macros.xml --- a/macros.xml Tue Jan 31 12:39:05 2017 -0500 +++ b/macros.xml Sat Mar 11 17:54:47 2017 -0500 @@ -1,6 +1,5 @@ - - 1.3 + 1.3.1 @@ -11,13 +10,10 @@ - bcftools + bcftools - htslib - - samtools + htslib + @@ -48,20 +44,20 @@ ## May need to symlink input if there is an associated #set $input_vcf = 'input.vcf.gz' #if $input_file.is_of_type('vcf') - bgzip -c "$input_file" > $input_vcf && + bgzip -c '$input_file' > $input_vcf && bcftools index $input_vcf && #elif $input_file.is_of_type('vcf_bgzip') - ln -s "$input_file" $input_vcf + ln -s '$input_file' $input_vcf #elif $input_file.is_of_type('bcf') #set $input_vcf = 'input.bcf' - ln -s "$input_file" $input_vcf && + ln -s '$input_file' $input_vcf && #if $input_file.metadata.bcf_index: - ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && + ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && #else bcftools index $input_vcf && #end if #elif $input_file.is_of_type('bcf_bgzip') - ln -s "$input_file" $input_vcf + ln -s '$input_file' $input_vcf #end if ]]> @@ -77,24 +73,23 @@ ## May need to symlink input if there is an associated #set $input_vcfs = [] #set $vcfs_list_file = 'vcfs_list' -#for (i,input_file) in enumerate($input_files): +#for (i, input_file) in enumerate($input_files): #set $input_vcf = 'input' + str($i) + '.vcf.gz' #if $input_file.is_of_type('vcf') - bgzip -c "$input_file" > $input_vcf && + bgzip -c '$input_file' > $input_vcf && bcftools index $input_vcf && #elif $input_file.is_of_type('vcf_bgz') - ln -s "$input_file" $input_vcf + ln -s '$input_file' $input_vcf #elif $input_file.is_of_type('bcf') #set $input_vcf = 'input' + str($i) + '.bcf.gz' - ## bgzip -c "$input_file" > $input_vcf && - ln -s "$input_file" $input_vcf && + ln -s '$input_file' $input_vcf && #if $input_file.metadata.bcf_index: - ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && + ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && #else bcftools index $input_vcf && #end if #elif $input_file.is_of_type('bcfvcf_bgz') - ln -s "$input_file" $input_vcf && + ln -s '$input_file' $input_vcf && #end if echo '$input_vcf' >> $vcfs_list_file && $input_vcfs.append($input_vcf) @@ -109,23 +104,23 @@ - + #if $input_fa_ref is not None: - --fasta-ref "$input_fa_ref" + --fasta-ref $input_fa_ref #elif 'fasta_ref' in $section and $section.fasta_ref: - --fasta-ref "${section.fasta_ref}" + --fasta-ref '${section.fasta_ref}' #end if @@ -151,24 +146,24 @@ - + #if 'AF_file' in $section and $section.AF_file: - --AF-file "${section.AF_file}" + --AF-file '${section.AF_file}' #end if - + #if 'estimate_AF' in $section and $section.estimate_AF: @@ -222,7 +217,7 @@ #if $section.collapse: - --collapse "${section.collapse}" + --collapse ${section.collapse} #end if @@ -234,7 +229,7 @@ #if $section.apply_filters: - --apply-filters "${section.apply_filters}" + --apply-filters '${section.apply_filters}' #end if @@ -286,9 +281,9 @@ #if $section.regions.regions_src == 'regions' and $section.regions.regions != '': - --regions "$section.regions.regions" + --regions '$section.regions.regions' #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: - --regions-file "$section.regions.regions_file" + --regions-file '$section.regions.regions_file' #end if @@ -351,7 +346,7 @@ --targets-file "${section.targets.invert_targets_file}${targets_path}" #else: #if $section.targets.targets_src == 'targets' and $section.targets.targets != '': - --targets "${section.targets.invert_targets_file}${section.targets.targets}" + --targets '${section.targets.invert_targets_file}${section.targets.targets}' #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" #end if @@ -375,7 +370,7 @@ #set $samples_defined = False #if str($section.samples) != '': #set $samples_defined = True - --samples "${section.invert_samples}${section.samples}" + --samples '${section.invert_samples}${section.samples}' #end if #if $section.samples_file: #set $samples_defined = True @@ -388,7 +383,7 @@ #if $section.sample: - --sample "${section.sample}" + --sample '${section.sample}' #end if @@ -425,7 +420,7 @@ #if $section.columns != '': - --columns "${section.columns}" + --columns '${section.columns}' #end if @@ -453,8 +448,7 @@ This Galaxy tool recommends using the compressed BCF format as piping is not implemented, and uncompressed data would use unnecessary amounts of space. - -]]> + ]]> + ]]> @@ -666,10 +658,5 @@ ID=@file .. selects lines with ID present in the file ID!=@~/file .. skip lines with ID present in the ~/file MAF[0]<0.05 .. select rare variants at 5% cutoff - -]]> - - - - + ]]> diff -r 45bbee210793 -r 788510a3597a tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 31 12:39:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - - - - - - - - -