| Previous changeset 3:cde34352778e (2017-01-31) Next changeset 5:741a08398a04 (2017-04-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 |
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modified:
README.md bcftools_view.xml macros.xml |
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removed:
tool_dependencies.xml |
| b |
| diff -r cde34352778e -r 993ed534cc38 README.md --- a/README.md Tue Jan 31 12:46:58 2017 -0500 +++ b/README.md Sat Mar 11 18:05:59 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r cde34352778e -r 993ed534cc38 bcftools_view.xml --- a/bcftools_view.xml Tue Jan 31 12:46:58 2017 -0500 +++ b/bcftools_view.xml Sat Mar 11 18:05:59 2017 -0500 |
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| b'@@ -1,5 +1,5 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">\n <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>\n <macros>\n <token name="@EXECUTABLE@">view</token>\n@@ -31,36 +31,36 @@\n \n ## Filter section\n #set $section = $sec_filter\n-#if $section.min_ac:\n- --min-ac "${section.min_ac}"\n+#if str($section.min_ac)\n+ --min-ac ${section.min_ac}\n #end if\n-#if $section.max_ac:\n- --max-ac "${section.max_ac}"\n+#if str($section.max_ac)\n+ --max-ac ${section.max_ac}\n #end if\n #if str($section.select_genotype) != "__none__":\n --genotype "${section.select_genotype}"\n #end if\n ## known or novel\n #if $section.known_or_novel:\n-${section.known_or_novel}\n+ ${section.known_or_novel}\n #end if\n-#if $section.min_alleles:\n- --min-alleles "${section.min_alleles}"\n+#if str($section.min_alleles)\n+ --min-alleles ${section.min_alleles}\n #end if\n-#if $section.max_alleles:\n- --max-alleles "${section.max_alleles}"\n+#if str($section.max_alleles)\n+ --max-alleles ${section.max_alleles}\n #end if\n #if $section.phased:\n-${section.phased}\n+ ${section.phased}\n #end if\n-#if $section.min_af:\n- --min-af "${section.min_af}"\n+#if str($section.min_af)\n+ --min-af ${section.min_af}\n #end if\n-#if $section.max_af:\n- --max-af "${section.max_af}"\n+#if str($section.max_af)\n+ --max-af ${section.max_af}\n #end if\n #if $section.uncalled:\n-${section.uncalled}\n+ ${section.uncalled}\n #end if\n #if $section.types:\n --types "${section.types}"\n@@ -69,17 +69,17 @@\n --exclude-types "${section.exclude_types}"\n #end if\n #if $section.private:\n-${section.private}\n+ ${section.private}\n #end if\n \n ## Output section\n #set $section = $sec_output\n ${section.drop_genotypes}\n #if $section.header:\n-${section.header}\n+ ${section.header}\n #end if\n-#if $section.compression_level:\n- --compression-level "${section.compression_level}"\n+#if str($section.compression_level)\n+ --compression-level ${section.compression_level}\n #end if\n \n #set $section = $sec_restrict\n@@ -94,7 +94,7 @@\n \n ## Primary Input/Outputs\n @INPUT_FILE@\n-> "$output_file"\n+> \'$output_file\'\n ]]>\n </command>\n <inputs>\n@@ -108,17 +108,17 @@\n </section>\n <section name="sec_subset" expanded="false" title="Subset Options">\n <expand macro="macro_samples" />\n- <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" \n+ <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"\n help="Only warn about unknown subset samples" />\n- <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update" \n+ <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"\n help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />\n- <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles" \n+ <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"\n help="Trim alternate alleles not seen in the subset" />\n </section>\n <section name="sec_filter" expanded="false" title="Filter Options">\n- <param name="min_ac" type="integer" label="Min Ac" optional="True" \n+ <param name="min_ac" type="integer" label="Min Ac" optional="True"\n help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />\n- <param name="max_ac" type="integer" label="Max Ac" optional="True" \n+ <param name="max_ac" ty'..b'">\n <assert_contents>\n- <has_text text="8657215" /> \n- <not_has_text text="rs6111385" /> \n+ <has_text text="8657215" />\n+ <not_has_text text="rs6111385" />\n </assert_contents>\n </output>\n </test>\n@@ -240,8 +240,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="rs6111385" /> \n- <not_has_text text="8657215" /> \n+ <has_text text="rs6111385" />\n+ <not_has_text text="8657215" />\n </assert_contents>\n </output>\n </test>\n@@ -252,8 +252,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="rs62584840" /> \n- <not_has_text text="8657215" /> \n+ <has_text text="rs62584840" />\n+ <not_has_text text="8657215" />\n </assert_contents>\n </output>\n </test>\n@@ -263,8 +263,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="rs5939407" /> \n- <not_has_text text="8657215" /> \n+ <has_text text="rs5939407" />\n+ <not_has_text text="8657215" />\n </assert_contents>\n </output>\n </test>\n@@ -274,8 +274,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="rs78249411" /> \n- <not_has_text text="rs6111385" /> \n+ <has_text text="rs78249411" />\n+ <not_has_text text="rs6111385" />\n </assert_contents>\n </output>\n </test>\n@@ -285,8 +285,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="rs6111385" /> \n- <not_has_text text="rs78249411" /> \n+ <has_text text="rs6111385" />\n+ <not_has_text text="rs78249411" />\n </assert_contents>\n </output>\n </test>\n@@ -300,8 +300,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <has_text text="##bcftools_viewCommand" /> \n- <not_has_text text="rs78249411" /> \n+ <has_text text="##bcftools_viewCommand" />\n+ <not_has_text text="rs78249411" />\n </assert_contents>\n </output>\n </test>\n@@ -312,8 +312,8 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <not_has_text text="##bcftools_viewCommand" /> \n- <has_text text="5464562" /> \n+ <not_has_text text="##bcftools_viewCommand" />\n+ <has_text text="5464562" />\n </assert_contents>\n </output>\n </test>\n@@ -324,9 +324,9 @@\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n- <not_has_text text="##FORMAT=<ID=GT" /> \n- <not_has_text text="rs62584840" /> \n- <has_text text="2343543" /> \n+ <not_has_text text="##FORMAT=<ID=GT" />\n+ <not_has_text text="rs62584840" />\n+ <has_text text="2343543" />\n </assert_contents>\n </output>\n </test>\n' |
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| diff -r cde34352778e -r 993ed534cc38 macros.xml --- a/macros.xml Tue Jan 31 12:46:58 2017 -0500 +++ b/macros.xml Sat Mar 11 18:05:59 2017 -0500 |
| [ |
| b'@@ -1,6 +1,5 @@\n-\n <macros>\n- <token name="@VERSION@">1.3</token>\n+ <token name="@VERSION@">1.3.1</token>\n <xml name="stdio">\n <stdio>\n <exit_code range="1:" />\n@@ -11,13 +10,10 @@\n </xml>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.3">bcftools</requirement>\n+ <requirement type="package" version="1.3.1">bcftools</requirement>\n <!-- conda dependency -->\n- <requirement type="package" version="1.3">htslib</requirement>\n- <!-- htslib provides tabix and bgzip\n- <requirement type="package" version="0.2.6">tabix</requirement>\n- -->\n- <requirement type="package" version="1.2">samtools</requirement>\n+ <requirement type="package" version="1.3.2">htslib</requirement>\n+ <yield />\n </requirements>\n </xml>\n <xml name="version_command">\n@@ -48,20 +44,20 @@\n ## May need to symlink input if there is an associated\n #set $input_vcf = \'input.vcf.gz\'\n #if $input_file.is_of_type(\'vcf\')\n- bgzip -c "$input_file" > $input_vcf &&\n+ bgzip -c \'$input_file\' > $input_vcf &&\n bcftools index $input_vcf &&\n #elif $input_file.is_of_type(\'vcf_bgzip\')\n- ln -s "$input_file" $input_vcf\n+ ln -s \'$input_file\' $input_vcf\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input.bcf\'\n- ln -s "$input_file" $input_vcf &&\n+ ln -s \'$input_file\' $input_vcf &&\n #if $input_file.metadata.bcf_index:\n- ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&\n+ ln -s \'${input_file.metadata.bcf_index}\' ${input_vcf}.csi &&\n #else\n bcftools index $input_vcf &&\n #end if\n #elif $input_file.is_of_type(\'bcf_bgzip\')\n- ln -s "$input_file" $input_vcf\n+ ln -s \'$input_file\' $input_vcf\n #end if\n ]]>\n </token>\n@@ -77,24 +73,23 @@\n ## May need to symlink input if there is an associated\n #set $input_vcfs = []\n #set $vcfs_list_file = \'vcfs_list\'\n-#for (i,input_file) in enumerate($input_files):\n+#for (i, input_file) in enumerate($input_files):\n #set $input_vcf = \'input\' + str($i) + \'.vcf.gz\'\n #if $input_file.is_of_type(\'vcf\')\n- bgzip -c "$input_file" > $input_vcf &&\n+ bgzip -c \'$input_file\' > $input_vcf &&\n bcftools index $input_vcf &&\n #elif $input_file.is_of_type(\'vcf_bgz\')\n- ln -s "$input_file" $input_vcf\n+ ln -s \'$input_file\' $input_vcf\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input\' + str($i) + \'.bcf.gz\'\n- ## bgzip -c "$input_file" > $input_vcf &&\n- ln -s "$input_file" $input_vcf &&\n+ ln -s \'$input_file\' $input_vcf &&\n #if $input_file.metadata.bcf_index:\n- ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&\n+ ln -s \'${input_file.metadata.bcf_index}\' ${input_vcf}.csi &&\n #else\n bcftools index $input_vcf &&\n #end if\n #elif $input_file.is_of_type(\'bcfvcf_bgz\')\n- ln -s "$input_file" $input_vcf &&\n+ ln -s \'$input_file\' $input_vcf &&\n #end if\n echo \'$input_vcf\' >> $vcfs_list_file &&\n $input_vcfs.append($input_vcf)\n@@ -109,23 +104,23 @@\n </token>\n \n <xml name="macro_fasta_ref">\n- <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />\n+ <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />\n </xml>\n <token name="@PREPARE_FASTA_REF@">\n <![CDATA[\n #set $input_fa_ref = None\n #if \'fasta_ref\' in $section and $section.fasta_ref:\n #set $input_fa_ref = \'ref.fa\'\n- ln -s $section.fasta_ref $input_fa_ref &&\n+ ln -s \'$section.fasta_ref\' $input_fa_ref &&\n samtools faidx $input_fa_ref &&\n #end if\n ]]>\n </token>\n <token name="@FASTA_REF@">\n #if $input_fa_ref is not None:\n- --fasta-ref "$input_fa_ref"\n+ --fasta-ref $input_fa_ref\n #elif \'fasta_ref\' in $section and $section.fasta_ref:\n- --fasta-ref "${section.fasta_ref}"\n+ --fasta-ref \'${section.fasta_ref}\'\n #end if\n </token>\n \n@@ -151,24 +146,24 @@\n \n \n <xml name="macro_AF_file">\n- <param name="AF_file" type="data" format="data'..b'<![CDATA[\n #if \'AF_file\' in $section and $section.AF_file:\n-#pass\n+ #pass\n #end if\n ]]>\n </token>\n <token name="@AF_FILE@">\n #if \'AF_file\' in $section and $section.AF_file:\n- --AF-file "${section.AF_file}"\n+ --AF-file \'${section.AF_file}\'\n #end if\n </token>\n \n <xml name="macro_estimate_AF">\n- <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" />\n+ <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" />\n </xml>\n <token name="@ESTIMATE_AF@">\n #if \'estimate_AF\' in $section and $section.estimate_AF:\n@@ -222,7 +217,7 @@\n </xml>\n <token name="@COLLAPSE@">\n #if $section.collapse:\n- --collapse "${section.collapse}"\n+ --collapse ${section.collapse}\n #end if\n </token>\n \n@@ -234,7 +229,7 @@\n </xml>\n <token name="@APPLY_FILTERS@">\n #if $section.apply_filters:\n- --apply-filters "${section.apply_filters}"\n+ --apply-filters \'${section.apply_filters}\'\n #end if\n </token>\n \n@@ -286,9 +281,9 @@\n </xml>\n <token name="@REGIONS@">\n #if $section.regions.regions_src == \'regions\' and $section.regions.regions != \'\':\n- --regions "$section.regions.regions"\n+ --regions \'$section.regions.regions\'\n #elif $section.regions.regions_src == \'regions_file\' and $section.regions.regions_file:\n- --regions-file "$section.regions.regions_file"\n+ --regions-file \'$section.regions.regions_file\'\n #end if\n </token>\n \n@@ -351,7 +346,7 @@\n --targets-file "${section.targets.invert_targets_file}${targets_path}"\n #else:\n #if $section.targets.targets_src == \'targets\' and $section.targets.targets != \'\':\n- --targets "${section.targets.invert_targets_file}${section.targets.targets}"\n+ --targets \'${section.targets.invert_targets_file}${section.targets.targets}\'\n #elif $section.targets.targets_src == \'targets_file\' and $section.targets.targets_file:\n --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"\n #end if\n@@ -375,7 +370,7 @@\n #set $samples_defined = False\n #if str($section.samples) != \'\':\n #set $samples_defined = True\n- --samples "${section.invert_samples}${section.samples}"\n+ --samples \'${section.invert_samples}${section.samples}\'\n #end if\n #if $section.samples_file:\n #set $samples_defined = True\n@@ -388,7 +383,7 @@\n </xml>\n <token name="@SAMPLE@">\n #if $section.sample:\n- --sample "${section.sample}"\n+ --sample \'${section.sample}\'\n #end if\n </token>\n \n@@ -425,7 +420,7 @@\n </xml>\n <token name="@COLUMNS@">\n #if $section.columns != \'\':\n- --columns "${section.columns}"\n+ --columns \'${section.columns}\'\n #end if\n </token>\n \n@@ -453,8 +448,7 @@\n This Galaxy tool recommends using the compressed BCF format\n as piping is not implemented, and uncompressed data would\n use unnecessary amounts of space.\n-\n-]]></token>\n+ ]]></token>\n <token name="@REGIONS_HELP@">\n <![CDATA[\n Region Selections\n@@ -475,8 +469,7 @@\n FILE. Note that overlapping regions in FILE can result in\n duplicated out of order positions in the output. This option\n requires indexed VCF/BCF files.\n-\n-]]></token>\n+ ]]></token>\n <token name="@TARGETS_HELP@"><![CDATA[\n Targets\n -------\n@@ -541,7 +534,6 @@\n | id | only records with identical ID column are compatible. |\n | | Supportedby bcftools merge only. |\n +------------+----------------------------------------------------------------+\n-\n </token>\n \n <token name="@EXPRESSIONS_HELP@">\n@@ -666,10 +658,5 @@\n ID=@file .. selects lines with ID present in the file\n ID!=@~/file .. skip lines with ID present in the ~/file\n MAF[0]<0.05 .. select rare variants at 5% cutoff\n-\n-]]></token>\n-\n-\n-\n-\n+ ]]></token>\n </macros>\n' |
| b |
| diff -r cde34352778e -r 993ed534cc38 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 31 12:46:58 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bcftools" version="1.3"> - <repository changeset_revision="43a9aebf3adb" name="package_bcftools_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="tabix" version="0.2.6"> - <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |