comparison raxml.xml @ 5:29ff6a849eac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 6e1b47bf8f06b9d92b369c2f36e52f4fc451d39c

4:73a469f7dc96

<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="8.2.4+galaxy2">
    <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
slots=\${GALAXY_SLOTS:-1};

            <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>

5:29ff6a849eac

<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
    <macros>
        <token name="@TOOL_VERSION@">8.2.4</token>
        <token name="@VERSION_SUFFIX@">3</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">raxml</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">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
slots=\${GALAXY_SLOTS:-1};

            <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" compare="re_match"/>
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Whale" />
                </assert_contents>
            </output>