comparison hyphy_absrel.xml @ 16:4cc4dbca2f02 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"

15:81e66674859e

<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            --alignment ./absrel_input.fa
            --tree ./absrel_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --output '$absrel_output'
            #if $log:
                > '$absrel_log'
            #end if
            ;
        @CATCH_MPIERR@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
    </inputs>
    <outputs>
        <data name="absrel_log" format="txt">
            <filter>log</filter>

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

16:4cc4dbca2f02

<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            --alignment ./absrel_input.fa
            --tree ./absrel_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --output '$absrel_output'
            --multiple-hits $multiple_hits
            #if $log:
                > '$absrel_log'
            #end if
            ;
        @CATCH_MPIERR@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <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_log" format="txt">
            <filter>log</filter>

    </outputs>
    <tests>
        <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="None" />
            <param name="log" value="false"/>
            <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="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[