comparison kmc_tools_transform.xml @ 2:c97f8a687258 draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty

1:c7fda6e88567

    <tests>
         <test>
             <!-- #1 test perform sort operation on KMC DB -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_suf" value="db.kmc_suf"/>
                    <element name="db.kmc_pre" value="db.kmc_pre"/>
                </collection>
	    </param>
            <conditional name="ops">
                   <param name="transform_operation" value="sort"/>
            </conditional>

        </test>
        <test>
             <!-- #2 test Generate Histogram Table -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_suf" value="db.kmc_suf"/>
                    <element name="db.kmc_pre" value="db.kmc_pre"/>
                </collection>
            </param>
            <conditional name="ops">
                   <param name="transform_operation" value="histogram"/>
            </conditional>

        </test>
        <test>
             <!-- #3 test Generate dump Table -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_suf" value="db.kmc_suf"/>
                    <element name="db.kmc_pre" value="db.kmc_pre"/>
                </collection>
            </param>
            <conditional name="ops">
                   <param name="transform_operation" value="dump"/>
            </conditional>

        </test>
        <test>
             <!-- #4 test perform reduce operation -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_suf" value="db.kmc_suf"/>
                    <element name="db.kmc_pre" value="db.kmc_pre"/>
                </collection>
	    </param>
	    <repeat name="operations">
                 <conditional name="ops">
                     <param name="transform_operation" value="reduce"/>

                 <section name="input_opt">
                    <param name="min_kmer_occurrence" value="4"/>
                    <param name="max_kmer_occurrence" value="40"/>
                 </section>
	    </repeat>
            <output_collection name="kmc_db" type="list">
                <element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>
		<element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
	        <element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
                <element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
		<element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/>
                <element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>
            </output_collection>
        </test>
      </tests>
    <help><![CDATA[

2:c97f8a687258

    <tests>
         <test>
             <!-- #1 test perform sort operation on KMC DB -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
                    <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
                </collection>
	    </param>
            <conditional name="ops">
                   <param name="transform_operation" value="sort"/>
            </conditional>

        </test>
        <test>
             <!-- #2 test Generate Histogram Table -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
                    <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
                </collection>
            </param>
            <conditional name="ops">
                   <param name="transform_operation" value="histogram"/>
            </conditional>

        </test>
        <test>
             <!-- #3 test Generate dump Table -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
                    <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
                </collection>
            </param>
            <conditional name="ops">
                   <param name="transform_operation" value="dump"/>
            </conditional>

        </test>
        <test>
             <!-- #4 test perform reduce operation -->
            <param name="input_collection">
                <collection type="list">
                    <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
                    <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
                </collection>
	    </param>
	    <repeat name="operations">
                 <conditional name="ops">
                     <param name="transform_operation" value="reduce"/>

                 <section name="input_opt">
                    <param name="min_kmer_occurrence" value="4"/>
                    <param name="max_kmer_occurrence" value="40"/>
                 </section>
	    </repeat>
	    <output_collection name="kmc_db" type="list">
		<element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>
		<element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/>
                <element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
		<element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>
	        <element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
                <element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
            </output_collection>
        </test>
      </tests>
    <help><![CDATA[