annotate data_manager/funannotate.xml @ 4:1c81a82b5b8e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

<tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <macros>
        <token name="@TOOL_VERSION@">1.8.15</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $wget:
            ## Asked for wget, we assume there's a certificate problem on (at least) one
            ## of the many requested servers, force disable of all checks
            echo "check_certificate = off" > \$HOME/.wgetrc &&
        #end if

        funannotate setup
            -d '$output_file.extra_files_path'
        #if $partial_data
            -i merops -b eukaryota
        #else
            -b all
        #end if
            $wget
        &&
        cp '$dmjson' '$output_file'
    ]]></command>
    <configfiles>
        <configfile name="dmjson"><![CDATA[
#from datetime import datetime
#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
    {
      "data_tables":{
        "funannotate":[
          {
            "value":"$version_id",
            "description":"Funannotate database $version_id",
            "format_version":"1.0",
            "path":"$output_file.extra_files_path"
          }
        ]
      }
    }]]></configfile>
    </configfiles>
    <inputs>
        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
        <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="partial_data" value="--partial"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="Funannotate database "/>
                    <has_text text='"format_version":"1.0"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="partial_data" value="--partial"/>
            <param name="wget" value="True"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="Funannotate database "/>
                    <has_text text='"format_version":"1.0"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        This data managers fetches data from various databases for the funannotate
        annotation tool and updates the funannotate data table.

        .. _funannotate: https://funannotate.readthedocs.io
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.4054262</citation>
    </citations>
</tool>