comparison hyphy_fel.xml @ 33:8a6ef85b934d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"

32:fc50c4bac0a3

<?xml version="1.0"?>
<tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09">
    <description>Fixed Effects Likelihood</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        @HYPHYMPI@ fel
            --alignment ./$input_file
            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --srv '$include_srv'
            --pvalue '$p_value'
            --output '$fel_output'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>

        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
        <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
            <option value="Yes">Yes (recommended)</option>
            <option value="No">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="fel_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
FEL : Fixed effects likelihood

33:8a6ef85b934d

<?xml version="1.0"?>
<tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09">
    <description>Fixed Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        @HYPHYMPI@ fel
            --alignment ./$input_file
            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --srv '$include_srv'
            --pvalue '$p_value'
            @resample@
            --precision $precision
            $ci
            --output '$fel_output'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>

        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
        <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
            <option value="Yes">Yes (recommended)</option>
            <option value="No">No</option>
        </param>
        <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" />
        <expand macro="resample"/>
        <param argument="--precision" type="select" label="Optimization precision for preliminary fits">
            <option value="standard">Standard</option>
            <option value="reduced">Reduced for faster fitting</option>
        </param>
    </inputs>
    <outputs>
        <data name="fel_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
        </test>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <param name="ci" value="true" />
            <param name="precision" value="reduced" />
            <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
FEL : Fixed effects likelihood