Mercurial > repos > iuc > bcftools_stats
changeset 19:a2f8dc22d7c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
| author | iuc |
|---|---|
| date | Thu, 12 Jan 2023 15:33:09 +0000 |
| parents | 388983871932 |
| children | bf8325a07ce7 |
| files | bcftools_stats.xml macros.xml |
| diffstat | 2 files changed, 16 insertions(+), 16 deletions(-) [+] |
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--- a/bcftools_stats.xml Thu Sep 29 09:04:17 2022 +0000 +++ b/bcftools_stats.xml Thu Jan 12 15:33:09 2023 +0000 @@ -9,7 +9,7 @@ <expand macro="requirements"> <expand macro="samtools_requirement"/> <expand macro="matplotlib_requirement" /> - <requirement type="package" version="0.8.0">tectonic</requirement> + <requirement type="package" version="0.12.0">tectonic</requirement> </expand> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @@ -89,13 +89,13 @@ <expand macro="macro_include" /> <expand macro="macro_exclude" /> </section> - <section name="sec_default" expanded="true" title="Stats Options"> - <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" - help="Include only 1st allele at multiallelic sites" /> + <section name="sec_default" expanded="true" title="Stats options"> + <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="First allele only" + help="Include only first allele at multiallelic sites" /> <conditional name="depth"> - <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]"> - <option value="no">use depth defaults</option> - <option value="yes">set depth</option> + <param name="set_depth" type="select" label="Depth distribution"> + <option value="no">Use depth defaults</option> + <option value="yes">Set depth values</option> </param> <when value="no"/> <when value="yes"> @@ -124,7 +124,7 @@ </when> </conditional> <expand macro="macro_exons_file" /> - <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" + <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split by ID (ignored on multiple inputs)" help="Collect stats for sites with ID separately (known vs novel)" /> <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" > @@ -132,21 +132,21 @@ </param> <conditional name="afbins"> <param name="afbins_select" type="select" label="Set af-bins"> - <option value="default">use default</option> - <option value="af_bins_list">enter bins</option> - <option value="af_bins_file">read bins from file</option> + <option value="default">Use default</option> + <option value="af_bins_list">Enter bins</option> + <option value="af_bins_file">Read bins from file</option> </param> <when value="default"/> <when value="af_bins_list"> - <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)"> - <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator> + <param name="af_bins_list" type="text" value="0.1,0.5,1" label="List of allele frequency bins" help="e.g. 0.1,0.5,1"> + <validator type="regex" message="Comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator> </param> </when> <when value="af_bins_file"> - <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/> + <param name="af_bins_file" type="data" format="tabular" label="File listing the allele frequency bins one per line"/> </when> </conditional> - <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT"> + <param name="af_tag" type="text" value="" optional="true" label="Allele frequency tag to use, by default estimated from AN,AC or GT"> <validator type="regex" message="TAG">^\w*$</validator> </param> <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
--- a/macros.xml Thu Sep 29 09:04:17 2022 +0000 +++ b/macros.xml Thu Jan 12 15:33:09 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.15.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.01</token> <xml name="bio_tools"> <xrefs>