comparison bcftools_stats.xml @ 19:a2f8dc22d7c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7

18:388983871932

    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
        <expand macro="matplotlib_requirement" />
        <requirement type="package" version="0.8.0">tectonic</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
#set $input_files = [$input_file]

            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <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" />
            <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>
                <when value="no"/>
                <when value="yes">
                    <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 
                    <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />

                <when value="history">
                    <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
                </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)" 
                   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]" >
                  <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
            </param>
            <conditional name="afbins">
                <param name="afbins_select" type="select" label="Set af-bins">
                    <option value="default">use default</option>
                    <option value="af_bins_list">enter bins</option>
                    <option value="af_bins_file">read bins from file</option>
                </param>
                <when value="default"/>
                <when value="af_bins_list">
                    <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)"> 
                        <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
                    </param>
                </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"/> 
                </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">
                  <validator type="regex" message="TAG">^\w*$</validator>
            </param>
            <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 
                   help="Produce verbose per-site and per-sample output" />
        </section>

19:a2f8dc22d7c0

    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
        <expand macro="matplotlib_requirement" />
        <requirement type="package" version="0.12.0">tectonic</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
#set $input_files = [$input_file]

            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <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="First allele only" 
                   help="Include only first allele at multiallelic sites" />
            <conditional name="depth">
                <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">
                    <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 
                    <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />

                <when value="history">
                    <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
                </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)" 
                   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]" >
                  <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
            </param>
            <conditional name="afbins">
                <param name="afbins_select" type="select" label="Set af-bins">
                    <option value="default">Use default</option>
                    <option value="af_bins_list">Enter bins</option>
                    <option value="af_bins_file">Read bins from file</option>
                </param>
                <when value="default"/>
                <when value="af_bins_list">
                    <param name="af_bins_list" type="text" value="0.1,0.5,1" label="List of allele frequency bins" help="e.g. 0.1,0.5,1"> 
                        <validator type="regex" message="Comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</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"/> 
                </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">
                  <validator type="regex" message="TAG">^\w*$</validator>
            </param>
            <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 
                   help="Produce verbose per-site and per-sample output" />
        </section>