comparison yahs.xml @ 2:fc925f53cae7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 73f497e595363dea7f041a4374c3a9518e7b9862

1:a3a92e30a727

<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</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.quality:
                -q $function.quality
            #end if
            $function.no_contig_ec
            $function.no_scaffold_ec
            -o yahs_out &&
            ls -lah &&
            python '$__tool_directory__/move_files.py'
            && ls -lah ./*
        #else:
            ln -s '$function.fasta' input.fasta &&
            ln -s '$function.agp' input.agp &&
            agp_to_fasta input.agp input.fasta
            #if $function.length:
                -l $function.length
            #end if
            -o output.fasta
        #end if
    ]]></command>
    <inputs>
        <conditional name="function">
            <param name="function_select" type="select" label="Which function would you like to run?">

                <conditional name="enzyme_conditional">
                    <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes.
                        The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual 
                        sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you 
                        use an enzyme-free prep, e.g. Omin-C.">
                        <option value="not_especified">Not especified</option>
                        <option value="preconfigured">Preconfigured restriction enzymes</option>
                        <option value="specific">Enter a specific sequence</option>
                    </param>
                    <when value="not_especified"/>
                    <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 name="agp" type="data" format="agp" label="Input AGP file"/>
                <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
                <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!-- INITIAL ROUNDS -->
        <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
            <filter>function['function_select'] == "yahs"</filter>

            <filter>function['function_select'] == "yahs"</filter>
        </data>
        <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
            <filter>function['function_select'] == "agp_to_fasta"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <conditional name="function">
                <param name="function_select" value="yahs"/>

                <param name="fasta" value="test.fasta"/>
                <param name="agp" value="test.agp"/>
                <param name="length" value="20"/>
            </conditional>
            <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
            <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 -->
        </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>

2:fc925f53cae7

<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</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.quality:
                -q $function.quality
            #end if
            $function.no_contig_ec
            $function.no_scaffold_ec
            -o yahs_out
            #if $log_out
                2> output.log
            #end if
            && ls -lah &&
            python '$__tool_directory__/move_files.py'
            && ls -lah ./*
        #else:
            ln -s '$function.fasta' input.fasta &&
            ln -s '$function.agp' input.agp &&
            agp_to_fasta input.agp input.fasta
            #if $function.length:
                -l $function.length
            #end if
            -o output.fasta
            #if $log_out:
                2> output.log
            #end if
        #end if
    ]]></command>
    <inputs>
        <conditional name="function">
            <param name="function_select" type="select" label="Which function would you like to run?">

                <conditional name="enzyme_conditional">
                    <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes.
                        The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual 
                        sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you 
                        use an enzyme-free prep, e.g. Omin-C.">
                        <option value="not_specified">Not specified</option>
                        <option value="preconfigured">Preconfigured restriction enzymes</option>
                        <option value="specific">Enter a specific sequence</option>
                    </param>
                    <when value="not_specified"/>
                    <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 name="agp" type="data" format="agp" label="Input AGP file"/>
                <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
                <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
            </when>
        </conditional>
        <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
    </inputs>
    <outputs>
        <!-- INITIAL ROUNDS -->
        <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
            <filter>function['function_select'] == "yahs"</filter>

            <filter>function['function_select'] == "yahs"</filter>
        </data>
        <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
            <filter>function['function_select'] == "agp_to_fasta"</filter>
        </data>
        <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
            <filter>log_out</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <conditional name="function">
                <param name="function_select" value="yahs"/>

                <param name="fasta" value="test.fasta"/>
                <param name="agp" value="test.agp"/>
                <param name="length" value="20"/>
            </conditional>
            <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
            <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
        </test>
        <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"/>
                <param name="agp" value="test.agp"/>
                <param name="res" value="50000,100000,150000,2000000,1000000"/>
            </conditional>
            <param name="log_out" value="yes"/>
            <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
            <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <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>