comparison hyphy_absrel.xml @ 33:212c958f6cee draft

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

32:3f59ebfbfe3d

<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        ln -s '$absrel_output' ${input_file}.aBSREL.json &&
        @HYPHYMPI@ absrel

            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --output '$absrel_output'
            --multiple-hits $multiple_hits
        @ERRORS@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
            <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
            <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
            <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
        </param>
        <expand macro="branches"/>
    </inputs>
    <outputs>
        <data name="absrel_output" format="hyphy_results.json" />
    </outputs>

        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <param name="multiple_hits" value="Double" />
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

aBSREL : Adaptive Branch-Site Random Effects Likelihood

33:212c958f6cee

<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        ln -s '$absrel_output' ${input_file}.aBSREL.json &&
        @HYPHYMPI@ absrel

            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --output '$absrel_output'
            --multiple-hits $multiple_hits
            $srv
        @ERRORS@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
            <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
            <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
            <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
        </param>
        <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
        <expand macro="branches"/>
    </inputs>
    <outputs>
        <data name="absrel_output" format="hyphy_results.json" />
    </outputs>

        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <param name="multiple_hits" value="Double" />
            <output name="absrel_output" file="absrel-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="multiple_hits" value="Double" />
            <param name="srv" value="--srv Yes" />
            <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

aBSREL : Adaptive Branch-Site Random Effects Likelihood