Mercurial > repos > iuc > bcftools_norm
changeset 3:a01eacacfd88 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
| author | iuc |
|---|---|
| date | Tue, 31 Jan 2017 12:43:24 -0500 |
| parents | d110fb275304 |
| children | 660f8eec689d |
| files | macros.xml |
| diffstat | 1 files changed, 24 insertions(+), 22 deletions(-) [+] |
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--- a/macros.xml Mon Oct 03 12:16:45 2016 -0400 +++ b/macros.xml Tue Jan 31 12:43:24 2017 -0500 @@ -14,14 +14,16 @@ <requirement type="package" version="1.3">bcftools</requirement> <!-- conda dependency --> <requirement type="package" version="1.3">htslib</requirement> + <!-- htslib provides tabix and bgzip <requirement type="package" version="0.2.6">tabix</requirement> + --> <requirement type="package" version="1.2">samtools</requirement> </requirements> </xml> <xml name="version_command"> <version_command>bcftools 2>&1 | grep 'Version:'</version_command> </xml> - + <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/btp352</citation> @@ -45,20 +47,20 @@ <![CDATA[ ## May need to symlink input if there is an associated #set $input_vcf = 'input.vcf.gz' -#if $input_file.datatype.file_ext == 'vcf' +#if $input_file.is_of_type('vcf') bgzip -c "$input_file" > $input_vcf && bcftools index $input_vcf && -#elif $input_file.datatype.file_ext == 'vcf_bgzip' +#elif $input_file.is_of_type('vcf_bgzip') ln -s "$input_file" $input_vcf -#elif $input_file.datatype.file_ext == 'bcf' +#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 && - #else + #else bcftools index $input_vcf && #end if -#elif $input_file.datatype.file_ext == 'bcf_bgzip' +#elif $input_file.is_of_type('bcf_bgzip') ln -s "$input_file" $input_vcf #end if ]]> @@ -77,21 +79,21 @@ #set $vcfs_list_file = 'vcfs_list' #for (i,input_file) in enumerate($input_files): #set $input_vcf = 'input' + str($i) + '.vcf.gz' - #if $input_file.datatype.file_ext == 'vcf' + #if $input_file.is_of_type('vcf') bgzip -c "$input_file" > $input_vcf && bcftools index $input_vcf && - #elif $input_file.datatype.file_ext == 'vcf_bgz' + #elif $input_file.is_of_type('vcf_bgz') ln -s "$input_file" $input_vcf - #elif $input_file.datatype.file_ext == 'bcf' + #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 && #if $input_file.metadata.bcf_index: ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && - #else + #else bcftools index $input_vcf && #end if - #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' + #elif $input_file.is_of_type('bcfvcf_bgz') ln -s "$input_file" $input_vcf && #end if echo '$input_vcf' >> $vcfs_list_file && @@ -225,7 +227,7 @@ </token> <xml name="macro_apply_filters"> - <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" + <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")"> <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> </param> @@ -272,7 +274,7 @@ </param> <when value="__none__"/> <when value="regions"> - <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" + <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" help="Each region is specifed as: chr or chr:pos or chr:from-to"> <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> </param> @@ -299,7 +301,7 @@ <token name="@PREPARE_TARGETS_FILE@"> <![CDATA[ #set $targets_path = None -#if 'targets' in $section +#if 'targets' in $section #if $section.targets.targets_src == 'targets_file': #set $targets_path = 'targets_file.tab.gz' bgzip -c "$section.targets.targets_file" > $targets_path && @@ -331,7 +333,7 @@ </param> <when value="__none__"/> <when value="targets"> - <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" + <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" help="Each target is specifed as: chr or chr:pos or chr:from-to"> <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> </param> @@ -358,15 +360,15 @@ </token> <xml name="macro_samples"> - <param name="samples" type="text" value="" label="Samples" optional="true" + <param name="samples" type="text" value="" label="Samples" optional="true" help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)"> <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> </param> - <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" + <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" help="inverts the query/filtering applied by Samples" /> - <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" + <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" help="(-S) file of samples to include" /> - <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" + <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" help="inverts the query/filtering applied by Samples File" /> </xml> <token name="@SAMPLES@"> @@ -416,7 +418,7 @@ </token> <xml name="macro_columns"> - <param name="columns" type="text" value="" label="Columns" optional="true" + <param name="columns" type="text" value="" label="Columns" optional="true" help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> </param> @@ -443,7 +445,7 @@ Output Type ----------- -Output compressed BCF (b), or uncompressed VCF (v). +Output compressed BCF (b), or uncompressed VCF (v). Use the BCF option when piping between bcftools subcommands to speed up performance by removing unecessary compression/decompression and VCF<->BCF conversion.