view data_manager/funannotate_options.xml @ 5:5459ec34767a draft default tip

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

+
−<tool id="data_manager_funannotate_options" name="Funannotate options 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 $test:
+
−            funannotate setup -d ./test/ -i busco busco_outgroups -b eukaryota > /dev/null &&
+
−            #set db_path="./test"
+
−        #else
+
−            #set db_path=$database.fields.path
+
−        #end if
+
−        python '$__tool_directory__/extract.py' '$db_path' '$database' '$output_file'
+
−    ]]></command>
+
−    <inputs>
+
−        <param name="test" type="hidden" value="" help="Used for testing"/>
+
−        <param name="database" label="Funannotate database" type="select">
+
−            <options from_data_table="funannotate">
+
−                <column name="value" index="0" />
+
−                <column name="name" index="1" />
+
−                <column name="path" index="3" />
+
−                <filter type="sort_by" column="0" reverse_sort_order="true"/>
+
−                <!-- <filter type="static_value" column="2" value="1.0" /> -->
+
−            </options>
+
−        </param>
+
−    </inputs>
+
−    <outputs>
+
−        <data name="output_file" format="data_manager_json"/>
+
−    </outputs>
+
−    <tests>
+
−        <test>
+
−            <param name="test" value="true"/>
+
−            <param name="database" value="test"/>
+
−            <output name="output_file">
+
−                <assert_contents>
+
−                    <has_text text="busco_db" n="1"/>
+
−                    <has_text text="outgroup" n="6"/>
+
−                    <has_text text="trained_species" n="166"/>
+
−                </assert_contents>
+
−            </output>
+
−            <assert_stdout>
+
−                <has_line line="1 x busco_db"/>
+
−                <has_line line="166 x trained_species"/>
+
−                <has_line line="6 x outgroup"/>
+
−            </assert_stdout>
+
−        </test>
+
−    </tests>
+
−    <help><![CDATA[
+
−        This data managers determines the options available in the select parameters of the funannotate tool
+
−        for a given funannotate DB in the funannotate data table
+
−
+
−        .. _funannotate: https://funannotate.readthedocs.io
+
−    ]]></help>
+
−    <citations>
+
−        <citation type="doi">10.5281/zenodo.4054262</citation>
+
−    </citations>
+
−</tool>