comparison raxml.xml @ 2:a4b71be30c3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"

1:ba29b5e2a4be

<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4">
    <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
    <requirements>
        <requirement type="package" version="8.2.4">raxml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
#set $slots = $getVar('GALAXY_SLOTS', 1)
#if $slots == 1:

        <test>
            <param name="extraOptions" value="required"/>
            <param name="infile" value="dna.phy"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" />
            <output name="bestTree">
                <assert_contents>
                    <has_text_matching expression="Frog" />
                </assert_contents>
            </output>
        </test>

            <param name="extraOptions" value="full"/>
            <param name="infile" value="dna.fasta"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <param name="number_of_runs" value="5"/>
            <output name="parsimonyTree">
                <assert_contents>
                    <has_text_matching expression="Chicken" />
                    <has_text_matching expression="RUN.4" />
                </assert_contents>
            </output>
            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/>
            <output name="bestTree">
                <assert_contents>
                    <has_text_matching expression="Whale" />
                </assert_contents>
            </output>
        </test>

2:a4b71be30c3c

<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
    <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
    <requirements>
        <requirement type="package" version="8.2.4">raxml</requirement>
        <requirement type="package" version="3.6">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
#set $slots = $getVar('GALAXY_SLOTS', 1)
#if $slots == 1:

        <test>
            <param name="extraOptions" value="required"/>
            <param name="infile" value="dna.phy"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Frog" />
                </assert_contents>
            </output>
        </test>

            <param name="extraOptions" value="full"/>
            <param name="infile" value="dna.fasta"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <param name="number_of_runs" value="5"/>
            <output name="parsimonyTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Chicken" />
                </assert_contents>
            </output>
            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx"/>
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Whale" />
                </assert_contents>
            </output>
        </test>