comparison macros.xml @ 33:e931e69b5a80 draft

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

32:d09dd951d0c4

<?xml version="1.0"?>
<macros>
    <xml name="inputs">
	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
        <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
    </xml>
    <xml name="bio_tools">

        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>
        </citations>
    </xml>
    <token name="@TOOL_VERSION@">2.5.31</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
            <yield/>
        </requirements>

    <xml name="alternative_model_output">
        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
            <filter>advanced['save_alternative_model']</filter>
        </data>
    </xml>
    <token name="@INPUT_TREE@"><![CDATA[
            #if $input_nhx:
                --tree input.nhx
            #end if
        ]]>

33:e931e69b5a80

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.5.36</token>
    <xml name="inputs">
	    <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
        <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
    </xml>
    <xml name="bio_tools">

        <citations>
            <citation type="doi">10.1093/molbev/msz197</citation>
            <yield/>
        </citations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
            <yield/>
        </requirements>

    <xml name="alternative_model_output">
        <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
            <filter>advanced['save_alternative_model']</filter>
        </data>
    </xml>
    <xml name="resample">
        <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." />
    </xml>
    <token name="@resample@"><![CDATA[
            #if $resample:
                --resample $resample
            #end if
        ]]>
    </token>

    <token name="@INPUT_TREE@"><![CDATA[
            #if $input_nhx:
                --tree input.nhx
            #end if
        ]]>