<tool id='ragtag' name='RagTag' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='20.01'>
    <description>reference-guided scaffolding of draft genomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs' />
    <expand macro='requirements' />
    <command detect_errors='exit_code'><![CDATA[
    #if $mode_conditional.mode_option != 'merge'
        #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
            #set $nucmer_params = '%s -l %s -c %s' % ($mode_conditional.advanced_options.mapping_conditional.anchor_mode,
                                                    $mode_conditional.advanced_options.mapping_conditional.l,
                                                    $mode_conditional.advanced_options.mapping_conditional.c)
        #end if
    #end if
    #if $mode_conditional.mode_option == 'merge'
    #set $input_files = list()
        mkdir merge_files &&
        #for $i, $j in enumerate($mode_conditional.scaffold_files)
            #set $out_file = './merge_files/scaffold_%s.agp' % $i
            ln -s '${j}' $out_file &&
            $input_files.append($out_file)
        #end for
        #set $merge_files = " ".join($input_files)
    #end if

    ## symlink reference because a .fai file is created
    #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch']
        ln -s '$mode_conditional.reference' reference.fa &&
        ln -s '$mode_conditional.query' query.fa &&
    #else
        ln -s '$assembly_fasta' assembly.fa &&
    #end if

    ragtag.py $mode_conditional.mode_option -u
    #if $mode_conditional.mode_option == 'correct'
        @INPUTS@
        @COMMON_PARAMETERS@
        #if $mode_conditional.validation_conditional.validation_option == 'true'
            -R '${mode_conditional.validation_conditional.R}'
            -T $mode_conditional.validation_conditional.read_type
            -v $mode_conditional.validation_conditional.v 
            #if $mode_conditional.validation_conditional.max_cov
                --max-cov $mode_conditional.validation_conditional.max_cov
            #end if
            #if $mode_conditional.validation_conditional.min_cov
                --min-cov $mode_conditional.validation_conditional.min_cov
            #end if
        #end if
        -b $mode_conditional.advanced_options.b
        #if $mode_conditional.advanced_options.missasembly_break
            $mode_conditional.advanced_options.missasembly_break
        #end if
        #if $mode_conditional.advanced_options.gff 
            --gff '${mode_conditional.advanced_options.gff}'
        #end if
        --read-aligner 'minimap2' ## it is the only allowed
    #else if $mode_conditional.mode_option == 'scaffold'
        @INPUTS@
        @COMMON_PARAMETERS@
        -i $mode_conditional.advanced_options.i
        -a $mode_conditional.advanced_options.a
        -s $mode_conditional.advanced_options.s
        #if $mode_conditional.advanced_options.gap_conditional.gap_option == 'true'
            -r
            -g '${mode_conditional.advanced_options.gap_conditional.g}'
            -m '${mode_conditional.advanced_options.gap_conditional.m}'
        #end if
        #if $mode_conditional.advanced_options.unplaced_conditional.unplaced_option == 'true'
            -C
            #if $mode_conditional.advanced_options.unplaced_conditional.J 
                -J '${mode_conditional.advanced_options.unplaced_conditional.J}'
            #end if
        #end if
    #else if $mode_conditional.mode_option == 'patch'
        @INPUTS@
        @COMMON_PARAMETERS@
        -s $mode_conditional.advanced_options.s
        -i $mode_conditional.advanced_options.i
        #if $mode_conditional.advanced_options.patching_mode
            $mode_conditional.advanced_options.patching_mode
        #end if
    #else
        assembly.fa
        #if $mode_conditional.scaffold_files
            $merge_files
        #end if
        #if $mode_conditional.merging_options.j
            -j $mode_conditional.merging_options.j
        #end if
        -l $mode_conditional.merging_options.l
        -e $mode_conditional.merging_options.e
        --gap-func $mode_conditional.merging_options.function_merging
        #if $mode_conditional.hic_options.b
            -b $mode_conditional.hic_options.b
            -r $mode_conditional.hic_options.r
            -p $mode_conditional.hic_options.p
        #end if 
    #end if
    -o ./
    #if $mode_conditional.mode_option != 'merge'
        -t \${GALAXY_SLOTS:-2}
    #end if
    #if $mode_conditional.mode_option == 'patch'
        && mv ragtag.patch.asm.paf.log ragtag.patch.log
    #end if
    ]]>    </command>
    <inputs>
        <conditional name="mode_conditional">
            <param name="mode_option" type="select" label="Operation mode">
                <option value="correct">Correct: homology-based missasembly correction</option>
                <option value="scaffold">Scaffold: homology-based assebly scaffolding</option>
                <option value="patch">Patch: homology-based assembly patching</option>
                <option value="merge">Merge: scaffolding merging</option>
            </param>
            <when value="correct">
                <expand macro="input_options"/>
                <conditional name="validation_conditional">
                    <param name="validation_option" type="select" label="Use validation reads">
                        <option value="true">Enabled</option>
                        <option value="false" selected="true">Disabled</option>
                    </param>
                    <when value="true">
                        <param argument="-R" type="data" format="fastq,fastqsanger" label="Validation reads" 
                            help="Without validation, the module will break at any point of reference discordance as defined by the 'correction options'. 
                                With validation, RagTag maps reads to the query assembly and verifies putative break points if they are near regions of 
                                exceptionally low or high coverage. The reads used for validation should come from the same genotype as the query 
                                assembly to ensure that coverage abnormalities don't arise from true biological variation" />
                        <param name="read_type" type="select" label="Read type">
                            <option value="sr">Illumina</option>
                            <option value="ont">Nanopore</option>
                            <option value="corr">Error corrected long-reads</option>
                        </param>
                        <param argument="-v" type="integer" min="0" value="10000" label="Coverage validation window size" 
                            help="This parameter specifies the window around the putative misassembly break point that RagTag examines 
                                for exceptionally low or high read coverage. The larger this window size, the more likely 
                                it is to find an unrelated coverage abnormality"/>
                        <param argument="--max-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or above this coverage level"/>
                        <param argument="--min-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or below this coverage level"/>
                    </when>
                    <when value="false"/>
                </conditional>
                <section name="advanced_options" title="Advanced options">
                    <expand macro="common_parameters"/>
                    <param argument="-b" type="integer" min="0" value="5000" label="Minimum break distance from contig ends"
                        help="Breaks will not be made within -b bp of query sequence termini"/>
                    <param name="missasembly_break" type="select" optional="true" label="Break misassebly option"
                        help="One can also direct RagTag to only break misassemblies between (--inter, query maps to >1 reference sequence) or within 
                            (--intra, query maps discordantly to 1 reference sequence) reference sequences">
                        <option value="--inter">Only break misassemblies between reference sequences (--inter)</option>
                        <option value="--intra">Only break missasemblies within reference sequences (--intra)</option>
                    </param>
                    <param argument="--gff" type="data" format="gff" optional="true" label="Don't break sequences within GFF intervals"
                        help=" If one has annotations associated with the query assembly, provide them with the --gff option to ensure that the query assembly 
                            is never broken within annotation intervals. "/>
                </section>
                <param name="output_correct" type="select"  multiple="true" label="Output files">
                    <option value="fasta" selected="true">The corrected query assembly in FASTA format</option>
                    <option value="agp" selected="true">The AGP file defining the exact coordinates of query sequence breaks</option>
                    <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
                    <option value="log">Log file</option>
                </param>
            </when>
            <when value="scaffold">
                <expand macro="input_options"/>
                <section name="advanced_options" title="advanced options">
                    <expand macro="common_parameters"/>
                    <param argument="-i" type="float" min="0" max="1" value="0.2" label="Minimum grouping confidence score"
                        help="The grouping confidence score is the number of base pairs a contig covered in its assigned reference chromosome 
                            divided by the total number of covered base pairs in the entire reference genome"/>
                    <param argument="-a" type="float" min="0" max="1" value="0" label="Minimum location confidence score"
                        help="To create a metric associated with contig ordering confidence, Ragtag define a location confidence. First, the smallest 
                            and largest alignment positions, with respect to the reference, between a contig and its assigned reference chromosome are found. 
                            The location confidence is then calculated as the number of covered base pairs in this range divided by the total number of 
                            base pairs in the range"/>
                    <param argument="-s" type="float" min="0" max="1" value="0" label="Minimum orientation confidence score"
                        help="To calculate the orientation confidence, each base pair in each alignment between a contig and its assigned reference chromosome 
                            casts a vote for the orientation of its alignment. The orientation confidence is the number of votes for the assigned orientation of 
                            the contig divided by the total number of votes"/>
                    <conditional name="gap_conditional">
                        <param name="gap_option" type="select" label="Infer gap sizes" help="When disabled, all gaps are 100 bp (-r)">
                            <option value="true" selected="true">Enabled</option>
                            <option value="false">Disabled</option>
                        </param>
                        <when value="true">
                            <param argument="-g" type="integer" min="0" value="100" label="Minimum infered gap size" />
                            <param argument="-m" type="integer" min="0" value="100000" label="Maximum inferred gap size"/>
                        </when>
                        <when value="false"/>
                    </conditional>
                    <conditional name="unplaced_conditional">
                        <param name="unplaced_option" type="select" label="Concatenate unplaced contigs and make 'chr0' (-C)">
                            <option value="true">Enabled</option>
                            <option value="false" selected="true">Disabled</option>
                        </param>
                        <when value="true">
                            <param argument="-J" type="data" format="txt" optional="true" label="List of query headers to leave unplaceds and exclude form 'chr0'"/>
                        </when>
                        <when value="false"/>
                    </conditional>
                </section>
                <param name="output_scaffold" type="select"  multiple="true" label="Output files">
                    <option value="fasta" selected="true">The scaffolds in FASTA format, defined by the ordering and orientations of the sequences containted in the AGP file</option>
                    <option value="agp" selected="true">The ordering and orientations of query sequences in AGP format</option>
                    <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
                    <option value="confidence">Confidence score values</option>
                    <option value="stats">Summary statistics for the scaffolding process</option>
                    <option value="log">Log file</option>
                </param>
            </when>
            <when value="patch">
                <expand macro="input_options"/>
                <section name="advanced_options" title="advanced options">
                    <expand macro="common_parameters"/>
                    <param argument="-s" type="integer" min="0" value="50000" label="Minimum merged alignment length" 
                        help="After merging, alignments less than -s bp long will be removed"/>
                    <param argument="-i" type="float" min="0" max="1" value="0.05" label="Maximum merged alignment distance" 
                        help="Maximum merged alignment distance from sequence terminus as fraction of the sequence length. Alignments must 
                        be within -i bp of a target sequence terminus or gap to be considered for patchin "/>
                    <param name="patching_mode" type="select" optional="true" label="Patching mode">
                        <option value="--fill-only">Only fill existing target gaps. Do not join target sequences</option>
                        <option value="--join_only">Only join and patch target sequences. DO not fill existing gaps</option>
                    </param>
                </section>
                <param name="output_patch" type="select"  multiple="true" label="Output files">
                    <option value="final_fasta" selected="true">The final FASTA file containing the patched assembly</option>
                    <option value="final_agp" selected="true">The final AGP file defining how final FASTA is built</option>
                    <option value="assembly_file" selected="true">Assembly alignment files</option>
                    <option value="split_assembly">The split target assembly and the renamed query assembly combined into one FASTA file</option>
                    <option value="split_description">An AGP file defining how the target assembly was split at gaps</option>
                    <option value="target_gaps">The target assembly split at gaps</option>
                    <option value="agp_renamed">An AGP file defining the new names for query sequences</option>
                    <option value="fasta_renamed">A FASTA file with the original query sequence, but with new names</option>
                    <option value="log">Log file</option>
                </param>
            </when>
            <when value="merge">
                <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/>
                <param name="scaffold_files" type="data" format="agp" multiple="true" optional="true" label="Scaffold AGP files"/>
                <section name="merging_options" title="Merging options">
                    <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/>
                    <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length" 
                        help="Assembly sequences shorter than -l will also be left unplaced."/>
                    <param argument="-e" type="float" min="0" value="0" label="Minimum edge weight" 
                        help="The edges in the merging graph represent scaffolding adjacencies. If an AGP file supports a particular adjacency, 
                            its weight is added to the edge weight. Any edges with a weight lower than the minimum edge weigth will be removed from the graph"/>
                    <param name="function_merging" type="select" label="Function for merging gap lengths" 
                        help="Scaffold gaps can differ between input AGP files. For example, a Hi-C derived AGP file might place 100 bp gaps between sequences 
                            while a reference-guided AGP file might infer gap sizes based on a reference genome. Use this parameter to specify how gap sizes 
                            should be computed from the supporting AGP files (--gap-func)">
                        <option value="min" selected="true">Min</option>
                        <option value="max">Max</option>
                        <option value="mean">Mean</option>
                    </param>
                </section>
                <section name="hic_options" title="HI-C options">
                    <param argument="-b" type="data" format="bam" optional="true" label="Hi-C alignments" help="Sorted by read name"/>
                    <param argument="-r" type="text" value="" optional="true" label="Restriction enzymes/sites or 'DNase'" help="List of restrction enzimes/sites or 'DNase', separated by comma. E.g. GATC,GACC">
                        <sanitizer invalid_char="">
                            <valid initial="string.letters,string.digits">
                                <add value="," />
                                <add value="[" />
                                <add value="]" />
                            </valid>
                        </sanitizer>
                        <validator type="regex">[0-9a-zA-Z,\]\[]+</validator>
                    </param>
                    <param argument="-p" type="float" min="0" max="1" value="1" optional="true" label="Portion of the sequence termini to consider for links"/>
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!--Correct mode outputs-->
        <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: PAF">
            <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter>
        </data>
        <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: AGP">
            <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter>
        </data>
        <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: FASTA">
            <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter>
        </data>
        <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: log">
            <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter>
        </data>
        <!--Scaffold mode outputs-->
        <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: PAF">
            <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter>
        </data>
        <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: AGP">
            <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter>
        </data>
        <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: FASTA">
            <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter>
        </data>
        <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: log">
            <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter>
        </data>
        <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: stats">
            <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter>
        </data>
        <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: confidence">
            <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter>
        </data>
        <!--Patch mode outputs-->
        <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: final AGP">
            <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: final PAF">
            <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: log">
            <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: components FASTA">
            <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: contigs AGP">
            <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: contigs FASTA">
            <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: final FASTA">
            <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: renamed AGP">
            <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter>
        </data>
        <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: renamed FASTA">
            <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter>
        </data>
        <!-- Merge mode outputs-->
        <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP">
            <filter>mode_conditional["mode_option"] == "merge"</filter>
        </data>
        <data format="fasta" name="merge_fasta" from_work_dir="ragtag.merge.fasta" label="${tool.name} on ${on_string}: merged FASTA">
            <filter>mode_conditional["mode_option"] == "merge"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <!--Test 01 correct mode minimap2-->
            <conditional name="mode_conditional">
                <param name="mode_option" value="correct"/>
                <param name="reference" value="genome.fna"/>
                <param name="query" value="contigs.fna"/>
                <param name="output_correct" value="fasta,agp,paf,log"/>
                <section name="advanced_options">
                    <param name="e" value="reference_headers_skip.txt"/>
                    <param name="j" value="query_headers_skip.txt"/>
                    <param name="f" value="1000"/>
                    <conditional name="mapping_conditional">
                        <param name="mapping_option" value="minimap2"/>
                        <param name="mm2_params" value="asm5"/>
                    </conditional>
                    <param name="remove_small" value="false"/>
                    <param name="q" value="10"/>
                    <param name="d" value="100000"/>
                    <param name="b" value="5000"/>
                    <param name="missasembly_break" value="--inter"/>
                    <param name="gff" value="annotation.gff"/>
                </section>
            </conditional>
            <output name="correct_paf" file="correct_paf_01.paf" ftype="paf"/>
            <output name="correct_agp" file="correct_agp_01.agp" ftype="agp"/>
            <output name="correct_fasta" file="correct_fasta_01.fasta" ftype="fasta"/>
            <output name="correct_log" file="correct_log_01.txt" ftype="txt" lines_diff="20"/>
        </test>
        <!--Test 02 correct mode nucmer-->
        <test expect_num_outputs="2">
            <conditional name="mode_conditional">
                <param name="mode_option" value="correct"/>
                <param name="reference" value="genome.fna"/>
                <param name="query" value="contigs.fna"/>
                <param name="output_correct" value="fasta,agp"/>
                <section name="advanced_options">
                    <param name="f" value="1000"/>
                    <conditional name="mapping_conditional">
                        <param name="mapping_option" value="nucmer"/>
                    </conditional>
                    <param name="remove_small" value="true"/>
                    <param name="q" value="10"/>
                    <param name="d" value="100000"/>
                    <param name="b" value="5000"/>
                    <param name="missasembly_break" value="--inter"/>
                </section>
            </conditional>
            <output name="correct_fasta" file="correct_fasta_02.fasta" ftype="fasta"/>
            <output name="correct_agp" file="correct_agp_02.agp" ftype="agp"/>

        </test>
        <!--Test 03 scaffold mode-->
        <test expect_num_outputs="6">
            <conditional name="mode_conditional">
                <param name="mode_option" value="scaffold"/>
                <param name="reference" value="genome.fna"/>
                <param name="query" value="contigs.fna"/>
                <param name="output_scaffold" value="fasta,agp,paf,confidence,log,stats"/>
                <section name="advanced_options">
                    <param name="f" value="1000"/>
                    <param name="remove_small" value="true"/>
                    <param name="q" value="10"/>
                    <param name="d" value="100000"/>
                    <param name="i" value="0.2"/>
                    <param name="a" value="0"/>
                    <param name="s" value="0"/>
                </section>
            </conditional>
            <output name="scaffold_paf" file="scaffold_paf_03.paf" ftype="paf"/>
            <output name="scaffold_agp" file="scaffold_apg.03.agp" ftype="agp"/>
            <output name="scaffold_fasta" file="scaffold_fasta_03.fasta" ftype="fasta"/>
            <output name="scaffold_log" file="scaffold_log_03.txt" ftype="txt" lines_diff="20"/>
            <output name="scaffold_stats" file="scaffold_stats_03.tabular" ftype="tabular"/>
            <output name="scaffold_confidence" file="scaffold_confidence_03.tabular" ftype="tabular"/>
        </test>
        <!--Test 04 patch mode-->
        <test expect_num_outputs="9">
            <conditional name="mode_conditional">
                <param name="mode_option" value="patch"/>
                <param name="reference" value="genome.fna"/>
                <param name="query" value="contigs.fna"/>
                <param name="output_patch" value="final_fasta,final_agp,assembly_file,split_assembly,split_description,target_gaps,agp_renamed,fasta_renamed,log"/>
                <section name="advanced_options">
                    <param name="s" value="50000"/>
                    <param name="i" value="0.05"/>
                </section>
            </conditional>
            <output name="patch_agp" file="patch_agp_04.agp" ftype="agp"/>
            <output name="patch_paf" file="patch_paf_04.paf" ftype="paf"/>
            <output name="patch_log" file="patch_log_04.txt" ftype="txt" lines_diff="20"/>
            <output name="patch_comps_fasta" ftype="fasta">
                <assert_contents>
                    <has_size value="603691" delta="100" />
                </assert_contents>
            </output>
            <output name="patch_ctg_fasta" file="patch_ctg_fasta_04.fasta" ftype="fasta"/>
            <output name="patch_ctg_agp" file="patch_ctg_fasta_04.agp" ftype="agp"/>
            <output name="patch_fasta" file="patch_fasta_04.fasta" ftype="fasta"/>
            <output name="patch_rename_agp" file="patch_rename_agp.agp" ftype="agp"/>
            <output name="patch_rename_fasta" file="patch_rename_fasta.fasta" ftype="fasta"/>
        </test>
        <test expect_num_outputs="2">
            <!-- Test 05 merge mode-->
            <conditional name="mode_conditional">
                <param name="mode_option" value="merge"/>
                <param name="assembly_fasta" value="correct_fasta_01.fasta"/>
                <param name="scaffold_files" value="correct_agp_01.agp,correct_agp_02.agp"/>
                <section name="merging_options">
                    <param name="l" value="100000"/>
                    <param name="e" value="0"/>
                    <param name="function_merging" value="min"/>
                </section>
            </conditional>
            <output name="merge_agp" file="merge_agp_05.agp" ftype="agp"/>
            <output name="merge_fasta" file="merge_fasta_05.fasta" ftype="fasta"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**Purpose**

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

- Homology-based misassembly correction
- Homology-based assembly scaffolding and patching
- Scaffold merging

----

.. class:: infomark

**Correct mode**

RagTag offers a correction module that uses a reference genome to identify and correct potential misassemblies in a query assembly. 
RagTag also provides the option to verify putative misassemblies by aligning reads (from the same genotype) to the query assembly 
and observing read coverage near misassembly break points. In all cases, sequence is never added or subtracted. Query sequences 
are only broken at points of putative misassembly.

*Misassemblies vs true variation*

Reference-guided misassembly signatures are sometimes caused by true biological structural variation if the reference and query assemblies 
represent distinct genotypes (or haplotypes). The read validation feature should help to avoid some of these misassembly false positives, 
and the validation sensitivity can be tuned with command line parameters. However, it is ultimately up to the discretion of the user to decide 
if misassembly correction is appropriate. One should validate all RagTag results with independent data (usually physical, optical, or genetic 
maps), when possible.

----

.. class:: infomark

**Scaffold mode**

Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of "N" characters) 
are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference 
assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.

----

.. class:: infomark

**Patch mode**

This mode uses one genome assembly to *patch* another genome assembly. We define two types of patches:

- Fills are patches that fill assembly gaps. This process is like traditional gap-filling, though it uses an assembly instead of WGS sequencing reads.
- Joins are patches that join distinct contigs. This is essentially scaffolding and gap-filling in a single step.

----

.. class:: infomark

**Merge mode**

Draft genome assemblies are often scaffolded multiple times using different approaches. For example, one might scaffold an assembly using different genome 
maps (physical, linkage, Hi-C, etc.), different methods, or different method parameters. RagTag merge is a tool to merge and reconcile different scaffoldings 
of the same assembly. In this way, one can leverage the advantages of multiple techniques to synergistically improve scaffolding.

Most tools write scaffolding results in the AGP file format, which encodes adjacency and gap information in a plain text file. To run RagTag merge, 
one must supply the assembly in FASTA format and at least two AGP files that define a scaffolding of the assembly. Each AGP file can optionally be 
assigned a weight, allowing users to assign the relative influence of each AGP on the final result.

If available, users can supply Hi-C alignments to the draft assembly to resolve conflicts in the merging graph. In this scenario, the input AGP 
files are used to build the initial graph, but then Hi-C alignments are used to re-weight the graph before computing the scaffolding solution.


**List of accepted restriction enzymes**

List of all accepted restriction enzymes and their restriction sites:

    - HindIII: AAGCTT
    - Sau3AI: GATC
    - MboI: GATC
    - DpnII: GATC
    - HinfI: GA[ATCG]TC
    - DdeI: CT[ATCG]AG
    - MseI: TTAA

For RagTag, use a comma separated list of enzymes or sites (or a mix). For example:

    - Arima Hi-C v1.0: *Sau3AI,HinfI* or *GATC,GA[ATCG]TC*
    - Arima Hi-C v2.0: *Sau3AI,HinfI,DdeI,MseI* or *GATC,GA[ATCG]TC,CT[ATCG]AG,TTAA*
 
 Note that for restriction sites, wildcards are represented with python regex syntax, not IUPAC ambiguity codes. e.g. '[ATCG]' instead of 'N'.
    
Restriction enzymes are not necessarily the enzyme used for sample prep. Each is only a enzyme that cuts at the corresponding restriction site.

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