comparison yahs.xml @ 4:425e63adcc5d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit be65e1846c9d4d63e80c01625e6e5f0d613948fe

3:39495e107274

<tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>yet another HI-C scaffolding tool</description>
    <macros>
        <token name="@VERSION@">1.2a.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">yahs</requirement>
        <requirement type="package" version="1.11">samtools</requirement>
        <requirement type="package" version="3.9">python</requirement>

            #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
                #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
                    -e 'GATC'
                #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
                    -e 'GATC,GANTC'
                #else
                    -e 'GATC,GANTC,CTNAG,TTAA'
                #end if
            #else if $function.enzyme_conditional.enzyme_options == 'specific':
                -e '${function.enzyme_conditional.manual_enzyme}'
            #end if
            #if $function.length:

                    <when value="preconfigured">
                        <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
                            <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
                            <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
                            <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
                        </param>
                    </when>
                    <when value="specific">
                        <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
                            help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">

                    <has_text text="[I::main] CMD: yahs"/>
                </assert_contents>
            </output>
            <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
        </test>
    </tests>
    <help><![CDATA[
        YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.
    ]]></help>
    <citations>

4:425e63adcc5d

<tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>yet another HI-C scaffolding tool</description>
    <macros>
        <token name="@VERSION@">1.2a.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">yahs</requirement>
        <requirement type="package" version="1.11">samtools</requirement>
        <requirement type="package" version="3.9">python</requirement>

            #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
                #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
                    -e 'GATC'
                #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
                    -e 'GATC,GANTC'
                #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2'
                    -e 'GATC,GANTC,CTNAG,TTAA'
                #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic'

                #end if
            #else if $function.enzyme_conditional.enzyme_options == 'specific':
                -e '${function.enzyme_conditional.manual_enzyme}'
            #end if
            #if $function.length:

                    <when value="preconfigured">
                        <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
                            <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
                            <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
                            <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
                            <option value="omnic">Dovetail Omni-C: enzyme-free prep</option>
                        </param>
                    </when>
                    <when value="specific">
                        <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
                            help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">

                    <has_text text="[I::main] CMD: yahs"/>
                </assert_contents>
            </output>
            <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
        </test>
        <!-- TEST 7: omnic prep -->
        <test expect_num_outputs="6">
            <conditional name="function">
                <param name="function_select" value="yahs"/>
                <param name="fasta" value="test.fasta"/>
                <param name="bfile" value="test.bed"/>
            </conditional>
            <conditional name="enzyme_conditional">
                <param name="enzyme_options" value="preconfigured"/>
                <param name="preconfigured_enzymes" value="omnic"/>
            </conditional>
            <param name="log_out" value="yes"/>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <not_has_text text="-e"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.
    ]]></help>
    <citations>