Mercurial > repos > iuc > bcftools_cnv
changeset 2:875003a6c2ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2017 06:51:30 -0500 |
| parents | 61b7d8323396 |
| children | 562d5787210c |
| files | bcftools_cnv.xml macros.xml |
| diffstat | 2 files changed, 27 insertions(+), 28 deletions(-) [+] |
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--- a/bcftools_cnv.xml Wed Jul 13 10:49:38 2016 -0400 +++ b/bcftools_cnv.xml Sat Jan 21 06:51:30 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>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description> <macros> <token name="@EXECUTABLE@">cnv</token> @@ -99,7 +99,7 @@ </section> <section name="sec_hmm" expanded="false" title="HMM Options"> <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" /> - <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" > + <param name="optimize" type="float" value="" min="0." max="1." label="Optimize" optional="True" > <help> Iteratively estimate the fraction of aberrant cells, down to the given fraction. Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise. @@ -111,7 +111,7 @@ Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. </help> </param> - <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True"> + <param name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9" optional="True"> <help> The HMM probability of transition to another copy number state. Increasing this value leads to smaller and more frequent calls. @@ -129,7 +129,7 @@ <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" help="Expected BAF deviation in control, defaults to: 0.04" /> - <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" > + <param name="LRR_weight" type="float" label="LRR Weight" optional="True" > <help> Relative contribution from LRR. With noisy data, this option can have big effect on the number of calls produced. @@ -141,7 +141,7 @@ help="Expected LRR deviation in query, default is: 0.2" /> <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" help="Expected LRR deviation in control, default is: 0.2" /> - <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True" + <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" value="10" optional="True" help="Window of LRR moving average smoothing" /> </section>
--- a/macros.xml Wed Jul 13 10:49:38 2016 -0400 +++ b/macros.xml Sat Jan 21 06:51:30 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.