comparison hyphy_slac.xml @ 26:0c6724c345d9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

25:d430eba4a90e

<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0" profile="19.09">
    <description>Single Likelihood Ancestor Counting</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">SLAC</token>
        <token name="@operation@">slac</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy slac
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --code '$gencodeid'
            --branches '$branches'
            --samples '$number_of_samples'
            --pvalue '$p_value'
            --output '$slac_output'
        > '$slac_log' ;
        @CATCH_ERROR@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
        <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value"  />
        <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
    </inputs>
    <outputs>
        <data name="slac_log" format="txt"/>
        <data name="slac_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>

26:0c6724c345d9

<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1" profile="19.09">
    <description>Single Likelihood Ancestor Counting</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        hyphy slac
            --alignment ./$input_file
            @INPUT_TREE@
            --code '$gencodeid'
            @branch_options@
            --samples '$number_of_samples'
            --pvalue '$p_value'
            --output '$slac_output'
        @ERRORS@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
        <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value"  />
        <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
    </inputs>
    <outputs>
        <data name="slac_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>