Mercurial > repos > iuc > bcftools_gtcheck
changeset 2:166520508473 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2017 06:52:48 -0500 |
| parents | d548c5551f01 |
| children | ad45a73c4042 |
| files | bcftools_gtcheck.xml macros.xml |
| diffstat | 2 files changed, 30 insertions(+), 30 deletions(-) [+] |
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--- a/bcftools_gtcheck.xml Wed Jul 13 10:50:59 2016 -0400 +++ b/bcftools_gtcheck.xml Sat Jan 21 06:52:48 2017 -0500 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1"> <description>Check sample identity</description> <macros> <token name="@EXECUTABLE@">gtcheck</token> @@ -15,16 +15,16 @@ #set $section = $sec_default #set $genotypes_vcf = None #if $section.genotypes: - #if $section.genotypes.datatype.file_ext == 'vcf' + #if $section.genotypes.is_of_type('vcf') #set $genotypes_vcf = 'genotypes.vcf.gz' bgzip -c "$section.genotypes" > $genotypes_vcf && bcftools index $genotypes_vcf && - #elif $section.genotypes.datatype.file_ext == 'bcf' + #elif $section.genotypes.is_of_type('bcf') #set $genotypes_vcf = 'genotypes.bcf' - ln -s "$ection.genotypes" $genotypes_vcf && + ln -s "$ection.genotypes" $genotypes_vcf && #if $section.genotypes.metadata.bcf_index: ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi && - #else + #else bcftools index $genotypes_vcf && #end if #end if @@ -80,10 +80,10 @@ <expand macro="macro_targets" /> </section> <section name="sec_default" expanded="true" title="Default Options"> - <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" + <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/> <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" /> - <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using <int> for unseen genotypes" /> + <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using <int> for unseen genotypes" /> <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" /> <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" /> <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" /> @@ -96,6 +96,7 @@ <tests> <test> <param name="input_file" ftype="vcf" value="view.vcf" /> + <param name="GTs_only" value="" /> <output name="output_file"> <assert_contents> <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
--- a/macros.xml Wed Jul 13 10:50:59 2016 -0400 +++ b/macros.xml Sat Jan 21 06:52:48 2017 -0500 @@ -21,7 +21,7 @@ <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 +45,20 @@ <![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 +77,21 @@ #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' >> $vcfs_list_file && @@ -225,7 +225,7 @@ </token> <xml name="macro_apply_filters"> - <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" + <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")"> <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> </param> @@ -272,7 +272,7 @@ </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 +299,7 @@ <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" > $targets_path && @@ -331,7 +331,7 @@ </param> <when value="__none__"/> <when value="targets"> - <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" + <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" help="Each target is specifed as: chr or chr:pos or chr:from-to"> <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> </param> @@ -339,7 +339,6 @@ </when> <when value="targets_file"> <expand macro="macro_targets_file"> - <optional>true</optional> </expand> </when> </conditional> @@ -359,15 +358,15 @@ </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+)*)?$</validator> </param> - <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" + <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" help="inverts the query/filtering applied by Samples" /> - <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" + <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" help="(-S) file of samples to include" /> - <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" + <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" help="inverts the query/filtering applied by Samples File" /> </xml> <token name="@SAMPLES@"> @@ -417,7 +416,7 @@ </token> <xml name="macro_columns"> - <param name="columns" type="text" value="" label="Columns" optional="true" + <param name="columns" type="text" value="" label="Columns" optional="true" help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> </param> @@ -444,7 +443,7 @@ 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.