comparison merqury.xml @ 1:39edec572bae draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"

0:9d79beb19ac3

<tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">
    <description>evaluate the assembly quality</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <version_command>merqury --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p output_files
        #if $mode.options == 'default'

                <valid initial="string.letters,string.digits">
                    <add value="_" />
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
        </collection>
        <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
        </collection>
        <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
        </collection>
        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
        </collection>
        <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
        </collection>
        <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="mode">
                <param name="options" value="trio"/>
                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_01"/>
            <output_collection name="png_files" type="list" count="3">
                <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_01.assembly.pat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_01.hapmers.blob" file="output_01.hapmers.blob.png" ftype="png">
                    <assert_contents>
                        <has_size value="10764" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="stats_files" type="list" count="2">
                <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
                <element name="output_01.completeness" ftype="tabular"/>
            </output_collection>
            <output_collection name="wig_files" type="list" count="2">
                <element name="output_01.assembly.pat" ftype="wig"/>
                <element name="output_01.assembly.mat" file="output_01.assembly.mat.wig" ftype="wig"/>
            </output_collection>
            <output_collection name="sizes_files" type="list" count="2">
                <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
                <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="bed_files" type="list" count="3">
                <element name="output_01.assembly.100_20000.phased_block" ftype="bed"/>
                <element name="output_01.assembly.100_20000.switch" ftype="bed"/>
                <element name="output_01.assembly.sort"/>
            </output_collection>
        </test>
        <test>
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_02"/>
            <output_collection name="png_files" type="list" count="6">
                <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="58059" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="57763" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="61814" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="64445" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="64795" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="66317" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="stats_files" type="list" count="1">
                <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>

                <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="wig_files" type="list" count="1">
                <element name="assembly_only" ftype="wig">
                    <assert_contents>
                        <has_size value="29909811" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="bed_files" type="list" count="1">
                <element name="assembly_only" ftype="bed">
                    <assert_contents>
                        <has_size value="73516121" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="two"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_03"/>
            <output_collection name="png_files" type="list" count="10">
                <element name="output_03.assembly_01.spectra-cn.fl" file="output_03.assembly_01.spectra-cn.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="58059" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.assembly_01.spectra-cn.ln" file="output_03.assembly_01.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="57763" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.assembly_01.spectra-cn.st" file="output_03.assembly_01.spectra-cn.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="61814" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.assembly_02.spectra-cn.fl" file="output_03.assembly_02.spectra-cn.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="61579" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.assembly_02.spectra-cn.ln" file="output_03.assembly_02.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="61538" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.assembly_02.spectra-cn.st" file="output_03.assembly_02.spectra-cn.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="67297" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.spectra-asm.ln" file="output_03.spectra-asm.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.spectra-cn.fl" file="output_03.spectra-cn.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="61397" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.spectra-cn.ln" file="output_03.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="61050" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_03.spectra-cn.st" file="output_03.spectra-cn.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="65243" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>    
            <output_collection name="stats_files" type="list" count="1">
                <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="qv_files" type="list" count="3">
                <element name="output_03.assembly_01" ftype="tabular"/>
                <element name="output_03.assembly_02" ftype="tabular"/>
                <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <conditional name="mode">
                <param name="options" value="trio"/>
                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_04"/>
            <output_collection name="png_files" type="list" count="5">
                <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="2733" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">
                    <assert_contents>
                        <has_size value="10764" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="stats_files" type="list" count="3">
                <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>
                <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>
                <element name="output_04.completeness"/>
            </output_collection>
            <output_collection name="qv_files" type="list" count="1">
                <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="wig_files" type="list" count="4">
                <element name="output_04.assembly_01.pat" ftype="wig"/>
                <element name="output_04.assembly_01.mat" ftype="wig"/>
                <element name="output_04.assembly_02.pat" ftype="wig"/>
                <element name="output_04.assembly_02.mat" ftype="wig"/>
            </output_collection>
            <output_collection name="sizes_files" type="list" count="4">
                <element name="output_04.assembly_01.100_20000.phased_block"/>
                <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>
                <element name="output_04.assembly_02.100_20000.phased_block"/>
                <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="bed_files" type="list" count="6">
                <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>
                <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>
                <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>
                <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>
                <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>
                <element name="output_04.assembly_02.sort" ftype="bed"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

1:39edec572bae

<tool id="merqury" name="Merqury" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>evaluate the assembly quality</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <version_command>merqury --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p output_files
        #if $mode.options == 'default'

                <valid initial="string.letters,string.digits">
                    <add value="_" />
                </valid>
            </sanitizer>
        </param>
        <param name="output_selector" type="select" display="checkboxes" multiple="true" optional="true" label="Output options">
            <option value="qv" selected="true">QV stats</option>
            <option value="plots" selected="true">Plots</option>
            <option value="sizes">Size files</option>
            <option value="stats" selected="true">Stats file</option>
            <option value="bed">BED: hap-mer tracks</option>
            <option value="wig">WIG: hap-mer tracks</option>
        </param>
    </inputs>
    <outputs>
        <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
            <filter>"bed" in output_selector</filter>
        </collection>
        <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.wig" format="wig" directory="output_files"/>
            <filter>"wig" in output_selector</filter>
        </collection>
        <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.qv" format="tabular" directory="output_files"/>
            <filter>"qv" in output_selector</filter>
        </collection>
        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
            <filter>"plots" in output_selector</filter>
        </collection>
        <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.sizes" format="tabular" directory="output_files"/>
            <filter>"sizes" in output_selector</filter>
        </collection>
        <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
            <filter>"stats" in output_selector</filter>
        </collection>
    </outputs>
    <tests>
        <!--Test 01: trio mode-->
        <test  expect_num_outputs="2">
            <conditional name="mode">
                <param name="options" value="trio"/>
                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_01"/>
            <param name="output_selector" value="sizes"/>
            <output_collection name="sizes_files" type="list" count="2">
                <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
                <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <!--Test 02: standard mode-->
        <test  expect_num_outputs="11">
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="one"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_02"/>
            <param name="output_selector" value="qv,png,bed,wig,sizes,stats"/>
            <param name="output_selector" value="plots,stats,wig,sizes,bed"/>
            <output_collection name="png_files" type="list" count="6">
                <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="71874" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="71888" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="71123" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
                    <assert_contents>
                        <has_size value="47245" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
                    <assert_contents>
                        <has_size value="46896" delta="100"/>
                    </assert_contents>
                </element>
                <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
                    <assert_contents>
                        <has_size value="45945" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="stats_files" type="list" count="1">
                <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>

                <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="wig_files" type="list" count="1">
                <element name="assembly_only" ftype="wig">
                    <assert_contents>
                        <has_size value="0"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="bed_files" type="list" count="1">
                <element name="assembly_only" ftype="bed">
                    <assert_contents>
                        <has_size value="0"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!--Test 03: Standard mode two assemblies-->
        <test  expect_num_outputs="4">
            <conditional name="mode">
                <param name="options" value="default"/>
                <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
                <conditional name="assembly_options">
                    <param name="number_assemblies" value="two"/>
                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_03"/>
            <param name="output_selector" value="qv,stats"/>
            <output_collection name="stats_files" type="list" count="1">
                <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
            </output_collection>
            <output_collection name="qv_files" type="list" count="3">
                <element name="output_03.assembly_01" ftype="tabular"/>
                <element name="output_03.assembly_02" ftype="tabular"/>
                <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <!--Test 04: trio mode two assemblies-->
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="options" value="trio"/>
                <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
                <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
                <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

                    <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
                    <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
                </conditional>
            </conditional>
            <param name="label" value="output_04"/>
            <param name="output_selector" value="qv"/>
            <output_collection name="qv_files" type="list" count="1">
                <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark