Mercurial > repos > jjohnson > bcftools_cnv
diff bcftools_cnv.xml @ 0:b50e0b926cde draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
| author | jjohnson |
|---|---|
| date | Sat, 25 Jun 2016 20:46:39 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_cnv.xml Sat Jun 25 20:46:39 2016 -0400 @@ -0,0 +1,176 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> + <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> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"><![CDATA[ +@PREPARE_ENV@ +@PREPARE_INPUT_FILE@ +#set $section = $sec_restrict +@PREPARE_TARGETS_FILE@ + +bcftools @EXECUTABLE@ + +--output-dir cnv_tmp + +## General section +#set $section = $sec_general +#if $section.control_sample: + --control-sample "${section.control_sample}" +#end if +#if $section.query_sample: + --query-sample "${section.query_sample}" +#end if +@AF_FILE@ + +#if $section.plot_threshold: + --plot-threshold "${section.plot_threshold}" +#end if + +## HMM section +#set $section = $sec_hmm +#if $section.aberrant_query or $section.aberrant_control: + #set $query_val = #if $section.aberrant_query then $section.aberrant_query else '1.0'# + #set $control_val = #if $section.aberrant_control then $section.aberrant_control else '1.0'# + --aberrant "${query_val},${control_val}" +#end if +#if $section.BAF_weight: + --BAF-weight "${section.BAF_weight}" +#end if +#if $section.BAF_dev_query or $section.BAF_dev_control: + #set $query_val = #if $section.BAF_dev_query then $section.BAF_dev_query else '1.0'# + #set $control_val = #if $section.BAF_dev_control then $section.BAF_dev_control else '1.0'# + --BAF-dev "${query_val},${control_val}" +#end if +#if $section.LRR_weight: + --LRR-weight "${section.LRR_weight}" +#end if +#if $section.LRR_dev_query or $section.LRR_dev_control: + #set $query_val = #if $section.LRR_dev_query then $section.LRR_dev_query else '1.0'# + #set $control_val = #if $section.LRR_dev_control then $section.LRR_dev_control else '1.0'# + --LRR-dev "${query_val},${control_val}" +#end if +#if $section.LRR_smooth_win: + --LRR-smooth-win "${section.LRR_smooth_win}" +#end if +#if $section.optimize: + --optimize "${section.optimize}" +#end if +#if $section.same_prob: + --same-prob "${section.same_prob}" +#end if +#if $section.err_prob: + --err-prob "${section.err_prob}" +#end if +#if $section.xy_prob: + --xy-prob "${section.xy_prob}" +#end if + +## Filter section +#set $section = $sec_restrict +@REGIONS@ +@TARGETS@ + +## Primary Input/Outputs +@INPUT_FILE@ +&& mv $output_dir/cn.*.tab "$output_cn" +&& mv $output_dir/dat.*.tab "$output_dat" +&& mv $output_dir/summary.*.tab "$output_summary" +## && python $output_dir/plot.*.py +]]> + </command> + <inputs> + <param name="output_dir" type="hidden" value="cnv_tmp"/> + <expand macro="macro_input" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_regions" /> + <expand macro="macro_targets" /> + </section> + <param name="reference_fasta" type="data" format="fasta" label="Reference Fasta" /> + <section name="sec_general" expanded="true" title="General Options"> + <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query samply name" /> + <param name="control_sample" type="text" label="Control Sample" optional="True" help="Optional control sample name to highlight differences" /> + <expand macro="macro_AF_file" /> + <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" /> + </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" > + <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. + </help> + </param> + <param name="same_prob" type="float" value="" min="0." max="1." label="Same Prob" optional="True"> + <help> + The prior probability of the query and the control sample being the same. + 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"> + <help> + The HMM probability of transition to another copy number state. + Increasing this value leads to smaller and more frequent calls. + </help> + </param> + + <param name="aberrant_query" type="float" value="" min="0." max="1." label="Aberrant Query" optional="true" + help="Fraction of aberrant cells in query, defaults to 1." /> + <param name="aberrant_control" type="float" value="" min="0." max="1." label="Aberrant Control" optional="true" + help="Fraction of aberrant cells in control, defaults to 1." /> + <param name="BAF_weight" type="float" value="1." min="0." max="1." label="Baf Weight" optional="True" help="relative contribution from BAF" /> + + <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" + help="Expected BAF deviation in query, defaults to: 0.04" /> + <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" > + <help> + Relative contribution from LRR. + With noisy data, this option can have big effect on the number of calls produced. + In truly random noise (such as in simulated data), the value should be set high (1.0), i + but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2). + </help> + </param> + <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" + 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" + help="Window of LRR moving average smoothing" /> + + </section> + </inputs> + <outputs> + <data name="output_cn" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.cn"/> + <data name="output_dat" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.dat"/> + <data name="output_summary" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.summary"/> + <!-- add plot output --> + <!-- script has png per chr, html of images or collect into pdf? + <data name="output_plots" format="" /> + --> + </outputs> + <tests /> + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ +===================================== + +Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR). +The HMM considers the following copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain) + +@REGIONS_HELP@ +@TARGETS_HELP@ + +@BCFTOOLS_MANPAGE@#@EXECUTABLE@ + +@BCFTOOLS_WIKI@ +]]> + </help> + <expand macro="citations" /> +</tool>