annotate gfastats.xml @ 9:f4a3eff8ab85 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 7de96873dbc693ce72d8d0aa734d1272a3d0f456

<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2">
    <description>The swiss army knife for Genome Assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <version_command>gfastats --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        gfastats
        '$input_file'
        #if $mode_condition.selector == 'statistics'
            #if $mode_condition.statistics_condition.selector == 'assembly'
                $mode_condition.statistics_condition.expected_genomesize
            #end if
        #end if
        #if $target_condition.target_option == 'true'
            $target_condition.target_sequence
            #if $target_condition.include_bed
                --include-bed $target_condition.include_bed
            #end if
            #if $target_condition.exclude_bed
                --exclude-bed $target_condition.exclude_bed
            #end if
        #end if
        #if $mode_condition.selector == 'manipulation'
            #if $mode_condition.swiss_army_knife
                -k $mode_condition.swiss_army_knife
            #end if
            #if $mode_condition.sort
                --sort $mode_condition.sort
            #end if
            #if $mode_condition.homopolymer_compress
                --homopolymer-compress $mode_condition.homopolymer_compress
            #end if
            $mode_condition.discover_paths
            $mode_condition.remove_terminal_gaps
            -o dataset.$mode_condition.output_condition.out_format
            #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz']
                #if $mode_condition.output_condition.line_length
                    --line-length $mode_condition.output_condition.line_length
                #end if
            #end if
            #if $mode_condition.output_condition.out_format in ['gfa','gfa.gz']
                #if $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_select == 'yes':
                --discover-terminal-overlaps $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_length
                #end if
            #end if
        #else if $mode_condition.selector == "statistics"
            #if $mode_condition.statistics_condition.selector == 'size'
                --out-size $mode_condition.statistics_condition.out_size
            #else if $mode_condition.statistics_condition.selector == 'coordinates'
                --out-coord $mode_condition.statistics_condition.out_coord
            #else if $mode_condition.statistics_condition.selector == 'assembly'
                --nstar-report
            #else
                --segment-report
                $mode_condition.statistics_condition.out_sequence
            #end if
            $mode_condition.locale
            $mode_condition.discover_paths
            $mode_condition.tabular > '$stats'
        #else
            --agp-to-path $mode_condition.agp_to_path
            $mode_condition.discover_paths
            -o dataset.gfa
        #end if
        --threads \${GALAXY_SLOTS:-8}
        #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
            && mv dataset* output_dataset
        #end if
    ]]></command>
    <inputs>
        <param name="input_file" argument="--fasta" type="data"
            format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz"
            label="Input file"/>
        <conditional name="target_condition">
            <param name="target_option" type="select" label="Specify target sequences">
                <option value="false">Disabled</option>
                <option value="true">Enabled</option>
            </param>
            <when value="false"/>
            <when value="true">
                <param name="target_sequence" type="text" value="" label="Target sequence" optional="true" help="Target specific sequence by header, optionally with coordinates: header[:start-end]">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits,string.letters">
                            <add value=":"/>
                            <add value="-"/>
                            <add value="_"/>
                            <add value="|"/>
                            <add value=" "/>
                        </valid>
                    </sanitizer>
                    <validator type="regex">[0-9A-Za-z:-_| ]+</validator>
                </param>
                <param argument="--include-bed" type="data" optional="true"
                    format="bed" label="Include specific intervals"
                    help="Generates output on a subset list of headers or coordinates   
                        in 0-based bed format. It can be combined with --exclude-bed. Optional."/>
                <param argument="--exclude-bed" type="data" format="bed" optional="true"
                    label="Exclude specific intervals"
                    help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed. Optional."/>
            </when>
            <when value="false"/>
        </conditional>
        <conditional name="mode_condition">
            <param name="selector" type="select" label="Tool mode">
                <option value="statistics">Summary statistics generation</option>
                <option value="manipulation">Genome assembly manipulation</option>
                <option value="scaffolding">Scaffolding</option>
            </param>
            <when value="manipulation">
                <param argument="--swiss-army-knife" type="data"
                    format="text" label="SAK input file" optional="true"
                    help="Set of instructions provided as an ordered list"/>
                <conditional name="output_condition">
                    <param argument="--out-format" type="select" 
                        label="Output format" help="Outputs selected sequences.">
                            <option value="fasta">FASTA</option>
                            <option value="fasta.gz">FASTA.gz</option>
                            <option value="fastq">FASTQ</option>
                            <option value="fastq.gz" selected="true">FASTQ.gz</option>
                            <option value="gfa">GFA</option>
                            <option value="gfa.gz">GFA.gz</option>
                    </param>
                    <when value="fasta">
                        <expand macro="length_macro"/>
                    </when>
                    <when value="fasta.gz">
                        <expand macro="length_macro"/>
                    </when>
                    <when value="fastq"/>
                    <when value="fastq.gz"/>
                    <when value="gfa">
                        <expand macro="terminal_overlaps_macro"/>
                    </when>
                    <when value="gfa.gz">
                        <expand macro="terminal_overlaps_macro"/>
                    </when>
		        </conditional>
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space, an assembly 
                    is a collection of segments and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence." />
                <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending uses the sequence/path header.">
                    <option value="" selected="true">Disabled</option>
                    <option value="ascending">Ascending</option>
                    <option value="descending">Descending</option>
                    <option value="largest">Largest</option>
                    <option value="smallest">Smallest</option>
                </param>
                <param argument="--remove-terminal-gaps" type="boolean" truevalue="--remove-terminal-gaps" falsevalue="" checked="false" label="Remove gaps from the beginning and end of sequences"/>
                <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." />
            </when>
            <when value="statistics">
                <conditional name="statistics_condition">
                    <param name="selector" type="select" label="Report mode">
                        <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option>
                        <option value="size">Scaffold, contig or gap sizes (--out-size)</option>
                        <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option>
                        <option value="sequence">Sequence statistics (--segment-report)</option>
                    </param>
                    <when value="size">
                        <param argument="--out-size" type="select" label="Feature for reporting sizes"
                            help="Generate a tabular file with the sequence sizes">
                            <option value="s">Scaffolds</option>
                            <option value="c">Contigs</option>
                            <option value="g">Gaps</option>
                        </param>
                    </when>
                    <when value="coordinates">
                        <param argument="--out-coord" type="select" label="BED coordinares feature"
                            help="Generates bed coordinates of given feature. Default: AGP">
                            <option value="a">AGP</option>
                            <option value="c">Contigs</option>
                            <option value="g">Gaps</option>
                        </param>
                    </when>
                    <when value="assembly">
                        <param name="expected_genomesize" type="integer" min="0" optional="true"
                            label="Expected genome size" help="Estimated genome size. This parameter is optional, but required for NG* statistics."/>
                    </when>
                    <when value="sequence">
                        <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false"
                            label="Report actual sequence" help="It reports also the actual sequence"/>
                    </when>
                </conditional>
                <param argument="--locale" type="boolean" truevalue="--locale en_US.UTF-8" falsevalue="" checked="true"
                    label="Thousands separator in output" help="Use commas for thousands separator in output?"/>
                <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
                    label="Tabular-format output" help="Generate output in tabular format"/>
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
            </when>
            <when value="scaffolding">
                <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" />
                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
            <filter>mode_condition['selector'] == 'statistics'</filter>
            <change_format>
                <when input="tabular" value="false" format="text"/>
            </change_format>
        </data>
        <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">
            <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter>
            <change_format>
                <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/>
                <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/>
                <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/>
                <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/>
                <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/>
                <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/>
                <when input="mode_condition.selector" value="scaffolding" format="gfa1"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <!--Test 01 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_01.fastq.gz"/>
            <conditional name="mode_condition">
                <param name="selector" value="manipulation"/>
                <param name="swiss_army_knife" value="swiss_army.sak"/>
                <conditional name="output_condition">
                    <param name="out_format" value="fasta.gz"/>
                </conditional>
            </conditional>
            <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/>
        </test>
        <!--Test 01 A) -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_01.fastq.gz"/>
            <conditional name="mode_condition">
                <param name="selector" value="manipulation"/>
                <param name="swiss_army_knife" value="swiss_army.sak"/>
                <param name="remove_terminal_gaps" value="true"/>
                <conditional name="output_condition">
                    <param name="out_format" value="fasta.gz"/>
                </conditional>
            </conditional>
            <output name="output" value="test_01_a.fasta.gz" ftype="fasta.gz"/>
        </test>
        <!--Test 02 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_01.fastq.gz"/>
            <conditional name="target_condition">
                <param name="target_condition" value="true"/>
                <param name="target_sequence" value="S1_1"/>
            </conditional>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="size"/>
                    <param name="out_size" value="c"/>
                </conditional>
                <param name="locale" value="false"/>
            </conditional>
            <output name="stats" ftype="tabular">
                <assert_contents>
                    <has_text text="S1_1.1&#009;8550" />
                </assert_contents>
            </output>
        </test>
        <!--Test 03 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_02.fasta.gz"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="sequence"/>
                </conditional>
                <param name="locale" value="false"/>
            </conditional>
            <output name="stats" ftype="tabular">
                <assert_contents>
                    <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1&#009;&#009;476&#009;198&#009;68&#009;93&#009;117&#009;33.82&#009;0" />
                </assert_contents>
            </output>
        </test>
        <!--Test 04 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_03.fasta"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="assembly"/>
                    <param name="expected_genomesize" value="600000"/>
                </conditional>
                <param name="locale" value="false"/>
            </conditional>
            <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>
        </test>
        <!--Test 05 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_04.gfa"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="coordinates"/>
                    <param name="out_coord" value="a"/>
                </conditional>
                <param name="locale" value="false"/>
            </conditional>
            <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>
        </test>
        <!--Test 06 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_04.gfa"/>
            <conditional name="mode_condition">
                <param name="selector" value="manipulation"/>
                <conditional name="output_condition">
                    <param name="out_format" value="fasta.gz"/>
                </conditional>
            </conditional>
            <output name="output" value="test_06.fasta.gz" ftype="fasta.gz"/>
        </test>
        <!--Test 07 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_03.fasta"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="assembly"/>
                </conditional>
                <param name="locale" value="false"/>
                <param name="tabular" value="false"/>
            </conditional>
            <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>
        </test>
        <!--Test 08 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_01.fastq.gz"/>
            <conditional name="mode_condition">
                <param name="selector" value="manipulation"/>
                <conditional name="output_condition">
                    <param name="out_format" value="fasta.gz"/>
                </conditional>
                <param name="sort" value="ascending"/>
            </conditional>
            <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/>
        </test>
        <!--Test 09 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_03.fasta"/>
            <conditional name="mode_condition">
                <param name="selector" value="manipulation"/>
                <conditional name="output_condition">
                    <param name="out_format" value="fasta.gz"/>
                </conditional>
                <param name="homopolymer_compress" value="10"/>
            </conditional>
            <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/>
        </test>
        <!--Test 10 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_04.gfa"/>
            <conditional name="mode_condition">
                <param name="selector" value="scaffolding"/>
                <param name="agp_to_path" value="dataset_05.agp"/>
                <param name="discover_paths" value="true"/>
            </conditional>
            <output name="output" value="test_10.gfa" ftype="gfa1"/>
        </test>
        <!--Test 11 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_03.fasta"/>
            <conditional name="target_condition">
                <param name="target_option" value="true"/>
                <param name="include_bed" value="regions.bed"/>
            </conditional>
            <conditional name="mode_condition">
                <param name="locale" value="false"/>
            </conditional>
            <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
        </test>
        <!--Test 12 -->
        <test expect_num_outputs="1">
            <param name="input_file" value="dataset_04.gfa"/>
            <conditional name="mode_condition">
                <param name="selector" value="statistics"/>
                <conditional name="statistics_condition">
                    <param name="selector" value="assembly"/>
                </conditional>
                <param name="locale" value="false"/>
                <param name="tabular" value="false"/>
                <param name="discover_paths" value="true"/>
            </conditional>
            <output name="stats" value="test_12_stats.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**Purpose**

gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless format conversion.


.. class:: infomark

**Metrics details**

Typical fast* metrics include:

- Scaffold, contig and gap size
- Number of scaffolds, contigs and gaps
- Total length of scaffolds, contigs and gaps
- Scaffold, contig, gap N50 and statistics (full N*/NG* statistics with the --nstar-report flag)
- Area under the curve (AuN/AuNG) values for scaffolds, contigs and gaps
- Average scaffold, contig, gap size
- Largest scaffold, contig and gap
- Base composition and GC content
- Soft-masked base counts (lower case bases)


Typical gfa metrics include:

- Number of nodes and edges
- Average degree
- Number of connected components, and length of the largets connected component
- Number of dead ends
- Number of disconnected components, and their total length


.. class:: infomark

**Assembly manipulation**

gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.

  ]]></help>
    <expand macro="citations"/>
</tool>