| Previous changeset 6:1f2183a23823 (2017-12-12) Next changeset 8:843e008b15fd (2019-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 |
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modified:
bcftools_convert_to_vcf.xml macros.xml test-data/view.bcf |
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added:
test-data/summary.pdf test-data/view.vcf_bgzip |
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removed:
test-data/view.bcf.csi |
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| diff -r 1f2183a23823 -r 367ba501b6eb bcftools_convert_to_vcf.xml --- a/bcftools_convert_to_vcf.xml Tue Dec 12 14:02:26 2017 -0500 +++ b/bcftools_convert_to_vcf.xml Thu Feb 21 16:05:01 2019 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@"> +<tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@"> <description>Converts other formats to VCF/BCFk</description> <macros> <token name="@EXECUTABLE@">convert</token> @@ -70,7 +70,7 @@ <expand macro="macro_columns"/> </when> <when value="gvcf"> - <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" /> + <param name="input_file" type="data" format="vcf" label="Genomic VCF (GATK HaplotypeCaller)" /> <expand macro="macro_fasta_ref" /> </when> <when value="gen_sample"> @@ -139,7 +139,7 @@ <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> - <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> + <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> </assert_contents> </output> </test> |
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| diff -r 1f2183a23823 -r 367ba501b6eb macros.xml --- a/macros.xml Tue Dec 12 14:02:26 2017 -0500 +++ b/macros.xml Thu Feb 21 16:05:01 2019 -0500 |
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| b'@@ -1,5 +1,5 @@\n <macros>\n- <token name="@VERSION@">1.4.0</token>\n+ <token name="@TOOL_VERSION@">1.9</token>\n <xml name="stdio">\n <stdio>\n <exit_code range="1:" />\n@@ -10,13 +10,13 @@\n </xml>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.4">bcftools</requirement>\n- <requirement type="package" version="1.4">htslib</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>\n+ <requirement type="package" version="1.9">htslib</requirement>\n <yield />\n </requirements>\n </xml>\n <xml name="samtools_requirement">\n- <requirement type="package" version="1.3.1">samtools</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n </xml>\n <xml name="version_command">\n <version_command>bcftools 2>&1 | grep \'Version:\'</version_command>\n@@ -39,7 +39,7 @@\n ]]>\n </token>\n <xml name="macro_input">\n- <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />\n+ <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />\n </xml>\n <token name="@PREPARE_INPUT_FILE@">\n <![CDATA[\n@@ -50,6 +50,11 @@\n bcftools index $input_vcf &&\n #elif $input_file.is_of_type(\'vcf_bgzip\')\n ln -s \'$input_file\' $input_vcf &&\n+ #if $input_file.metadata.tabix_index:\n+ ln -s \'${input_file.metadata.tabix_index}\' ${input_vcf}.tbi &&\n+ #else\n+ bcftools index $input_vcf &&\n+ #end if\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input.bcf\'\n ln -s \'$input_file\' $input_vcf &&\n@@ -58,8 +63,6 @@\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 #end if\n ]]>\n </token>\n@@ -68,7 +71,7 @@\n </token>\n \n <xml name="macro_inputs">\n- <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />\n+ <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />\n </xml>\n <token name="@PREPARE_INPUT_FILES@">\n <![CDATA[\n@@ -80,8 +83,13 @@\n #if $input_file.is_of_type(\'vcf\')\n bgzip -c \'$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+ #elif $input_file.is_of_type(\'vcf_bgzip\')\n+ ln -s \'$input_file\' $input_vcf &&\n+ #if $input_file.metadata.tabix_index:\n+ ln -s \'${input_file.metadata.tabix_index}\' ${input_vcf}.tbi &&\n+ #else\n+ bcftools index $input_vcf &&\n+ #end if\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input\' + str($i) + \'.bcf.gz\'\n ln -s \'$input_file\' $input_vcf &&\n@@ -90,8 +98,6 @@\n #else\n bcftools index $input_vcf &&\n #end if\n- #elif $input_file.is_of_type(\'bcfvcf_bgz\')\n- ln -s \'$input_file\' $input_vcf &&\n #end if\n echo \'$input_vcf\' >> $vcfs_list_file &&\n $input_vcfs.append($input_vcf)\n@@ -106,7 +112,7 @@\n </token>\n \n <xml name="macro_fasta_ref">\n- <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />\n+ <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />\n </xml>\n <token name="@PREPARE_FASTA_REF@">\n <![CDATA[\n@@ -148,7 +154,7 @@\n \n \n <xml name="macro_AF_file">\n- <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />\n+ <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />\n </xml>\n <!-- This may need to bgzip and tabix the file -->\n <token name="@PREPARE_AF_FILE@">\n@@ -165,7 +171,7 @@\n </token>\n \n <xml '..b'ne__"/>\n <when value="targets">\n- <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"\n+ <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"\n help="Each target is specifed as: chr or chr:pos or chr:from-to">\n <validator type="regex" message="">^(\\w+(:\\d+(-\\d+)?)?(,\\w+(:\\d+(-\\d+)?)?)*)?$</validator>\n </param>\n@@ -373,16 +379,16 @@\n </token>\n \n <xml name="macro_samples">\n- <param name="samples" type="text" value="" label="Samples" optional="true"\n- help="(-s) comma separated list of samples to annotate (or exclude)">\n+ <param argument="--samples" type="text" value="" optional="true" label="Samples"\n+ help="Comma separated list of samples to annotate (or exclude)">\n <validator type="regex" message="">^(\\w+(,\\w+)*)?$</validator>\n </param>\n <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"\n- help="inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />\n- <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"\n- help="(-S) file of samples to include" />\n- <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"\n- help="inverts the query/filtering applied by Samples File" />\n+ help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />\n+ <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"\n+ help="File of samples to include" />\n+ <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"\n+ help="inverts the query/filtering applied by Samples file" />\n </xml>\n <token name="@SAMPLES@">\n #set $samples_defined = False\n@@ -397,7 +403,7 @@\n </token>\n \n <xml name="macro_sample">\n- <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />\n+ <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />\n </xml>\n <token name="@SAMPLE@">\n #if $section.sample:\n@@ -407,7 +413,7 @@\n \n \n <xml name="macro_include">\n- <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">\n+ <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">\n <validator type="regex" message="Single quote not allowed">^[^\']*$</validator>\n <sanitizer sanitize="False"/>\n </param>\n@@ -419,7 +425,7 @@\n </token>\n \n <xml name="macro_exclude">\n- <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">\n+ <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">\n <validator type="regex" message="Single quote not allowed">^[^\']*$</validator>\n <sanitizer sanitize="False"/>\n </param>\n@@ -431,8 +437,8 @@\n </token>\n \n <xml name="macro_columns">\n- <param name="columns" type="text" value="" label="Columns" optional="true"\n- help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">\n+ <param name="columns" type="text" value="" optional="true" label="Columns"\n+ help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">\n <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>\n </param>\n </xml>\n' |
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