comparison kofamscan.xml @ 5:8ec7636fa875 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 1e2ca1537bd6d141a3494d6bb0a2f050082f7257

4:2eb7932e91a3

<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>gene function annotation based on KEGG orthology and HMM</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.0</token>
        <token name="@VERSION_SUFFIX@">3</token>
        <xml name="reportannotation" token_selected="">
            <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
        </xml>
    </macros>
    <xrefs>

                <option value="cached" selected="true">Cached</option>
                <option value="compressed">Compressed set of HMM and HAL file(s)</option>
                <option value="hmm">HMM file(s)</option>
            </param>
            <when value="cached">
                <param name="kofam" type="select">
                    <options from_data_table="kofam"/>
                </param>
                <param name="kofam_subset" type="select" optional="true">
                    <options from_data_table="kofam_subset">
                        <filter type="param_value" column="2" ref="kofam"/>
                        <filter type="sort_by" column="1"/>
                        <filter type="unique_value" column="1"/>
                        <column name="name" index="1"/>
                        <column name="value" index="0"/>
                    </options>
                    <validator type="no_options" message="No option available for this input"/>
                </param>
            </when>
            <when value="compressed">
                <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/>
                <param argument="-k" type="data" format="tabular" label="Select KO list file"/>

5:8ec7636fa875

<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>gene function annotation based on KEGG orthology and HMM</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.0</token>
        <token name="@VERSION_SUFFIX@">4</token>
        <xml name="reportannotation" token_selected="">
            <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
        </xml>
    </macros>
    <xrefs>

                <option value="cached" selected="true">Cached</option>
                <option value="compressed">Compressed set of HMM and HAL file(s)</option>
                <option value="hmm">HMM file(s)</option>
            </param>
            <when value="cached">
                <param name="kofam" type="select" label="Kofam database to use">
                    <options from_data_table="kofam"/>
                    <validator type="no_options" message="No option available for this input."/>
                </param>
                <param name="kofam_subset" type="select" optional="true" label="Use only a subset of the selected Kofam database" help="If nothing is selected the complete database is used">
                    <options from_data_table="kofam_subset">
                        <filter type="param_value" column="2" ref="kofam"/>
                        <filter type="sort_by" column="1"/>
                        <filter type="unique_value" column="1"/>
                        <column name="name" index="1"/>
                        <column name="value" index="0"/>
                    </options>
                </param>
            </when>
            <when value="compressed">
                <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/>
                <param argument="-k" type="data" format="tabular" label="Select KO list file"/>