comparison hyphy_busted.xml @ 24:e2f03a50aace draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

23:eb26b02af55a

<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09">
    <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' busted_input.fa &&
        ln -s '$input_nhx' busted_input.nhx &&
        hyphy busted
            --alignment ./busted_input.fa
            --tree ./busted_input.nhx
            --code $gencodeid
            --branches '$branches'
            --output '$busted_output'
            > '$busted_log'
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>

24:e2f03a50aace

<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09">
    <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">BUSTED</token>
        <token name="@operation@">busted</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy busted
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --code $gencodeid
            --branches '$branches'
            --output '$busted_output'
            > '$busted_log' ;
        @CATCH_ERROR@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>