comparison craq.xml @ 0:7895d95c01fa draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/craq commit fe19727db664bcad91b66546149cbf34a6a012e7

0:7895d95c01fa

<tool id="craq" name="CRAQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>assess the accuracy of assembled genomic sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ## Decision Tree to structure and prepare input files
        ## Craq expects sorted and indexed bam files
        cp '$genome' genome.fa &&

        ## Prepare SMS input
        #if $sms_input:
            #if $sms_input[0].is_of_type('bam'):
                cp '${sms_input[0]}' 'sms_sorted.bam' &&
                samtools index 'sms_sorted.bam' &&
            #else:
                #for $i, $f in enumerate($sms_input):
                    cp '$f' 'sms_${i}.${f.ext}' &&
                #end for
            #end if
        #end if

        ## Prepare NGS input
        #if $ngs_input:
            #if $ngs_input[0].is_of_type('bam'):
                cp '${ngs_input[0]}' 'ngs_sorted.bam' &&
                samtools index 'ngs_sorted.bam' &&
            #else:
                #for $i, $f in enumerate($ngs_input):
                    cp '$f' 'ngs_${i}.${f.ext}' &&
                #end for
            #end if
        #end if


        ## Build tool command line
        craq
        -g genome.fa

        ## SMS input
        #if $sms_input:
            -sms
            #if $sms_input[0].is_of_type('bam'):
                'sms_sorted.bam'
            #else:
                #set $sms_files = ','.join(['sms_%d.%s' % ($i, $f.ext) for $i, $f in enumerate($sms_input)])
                $sms_files
            #end if
        #end if

        ## NGS input
        #if $ngs_input:
            -ngs
            #if $ngs_input[0].is_of_type('bam'):
                'ngs_sorted.bam'
            #else:
                #set $ngs_files = ','.join(['ngs_%d.%s' % ($i, $f.ext) for $i, $f in enumerate($ngs_input)])
                $ngs_files
            #end if
        #end if

        ## Filter parameters
        -sn $filter_params.sn
        -sf $filter_params.sf
        -ln $filter_params.ln
        -lf $filter_params.lf
        -hmin $filter_params.hmin
        -hmax $filter_params.hmax
        -mgs $filter_params.mgs
        --sms_coverage $filter_params.sms_coverage
        --ngs_coverage $filter_params.ngs_coverage

        ## Other parameters
        $other_params.ser
        $other_params.snv
        --gapmodel $other_params.gapmodel
        $other_params.break
        --map $other_params.map
        --mapq $other_params.mapq
        --norm_window $other_params.norm_window
        --regional_window $other_params.regional_window
        $other_params.plot
        #if $other_params.plot_ids:
            --plot_ids $other_params.plot_ids
        #end if
        --thread "\${GALAXY_SLOTS:-8}"
        -D outputs
    ]]></command>
    <inputs>
        <param name="genome" type="data" label="Assembly sequence file" format="fasta" help="The genome assembly to be evaluated in FASTA format"/>
        <param name="sms_input" type="data" optional="true" multiple="true" label="SMS long-read alignment or sequences" format="bam,fastq,fastq.gz" help="Provide either a single BAM file OR multiple FASTQ files (uncompressed or gzipped). At least one of SMS or NGS input must be provided"/>
        <param name="ngs_input" type="data" optional="true" multiple="true" label="NGS short-read alignment or sequences" format="bam,fastq,fastq.gz" help="Provide either a single BAM file OR multiple FASTQ files (uncompressed or gzipped). At least one of SMS or NGS input must be provided"/>
        <section name="filter_params" title="Filter Parameters" expanded="False">
            <param argument="-sn" type="integer" min="0" value="2" label="Minimum number of NGS clipped-reads" help="Minimum number of NGS reads that must show clipping to flag potential errors"/>
            <param argument="-sf" type="float" min="0.0" max="1.0" value="0.75" label="Minimum proportion of NGS clipped-reads" help="Minimum proportion of NGS reads that must show clipping relative to total coverage"/>
            <param argument="-ln" type="integer" min="0" value="2" label="Minimum number of SMS clipped-reads" help="Minimum number of SMS long reads that must show clipping to flag potential errors"/>
            <param argument="-lf" type="float" min="0.0" max="1.0" value="0.75" label="Minimum proportion of SMS clipped-reads" help="Minimum proportion of SMS reads that must show clipping relative to total coverage"/>
            <param argument="-hmin" type="float" min="0.0" max="1.0" value="0.4" label="Lower clipping rate for heterozygous allele" help="Lower clipping rate threshold to identify heterozygous variants (CRHs)"/>
            <param argument="-hmax" type="float" min="0.0" max="1.0" value="0.6" label="Upper clipping rate for heterozygous allele" help="Upper clipping rate threshold to identify heterozygous variants (CRHs)"/>
            <param argument="-mgs" type="integer" min="1" value="10" label="Minimum gap size (bp)" help="Gap[N] sequences longer than this threshold will be treated as breakage"/>
            <param argument="--sms_coverage" type="integer" min="0" value="100" label="Average SMS coverage" help="Expected average SMS long-read coverage depth for normalization"/>
            <param argument="--ngs_coverage" type="integer" min="0" value="100" label="Average NGS coverage" help="Expected average NGS short-read coverage depth for normalization"/>
        </section>
        <section name="other_params" title="Other Parameters" expanded="False">
            <param argument="-ser" type="boolean" checked="true" truevalue="-ser T" falsevalue="" label="Search error regions near breakpoints" help="Search noisy error regions near CRE/CSE breakpoints"/>
            <param argument="-snv" type="boolean" checked="false" truevalue="-snv T" falsevalue="" label="Report SNV/heterozygous variants" help="Report tiny indel errors or heterozygous variants under 40bp.(Resource intensive)"/>
            <param argument="--gapmodel" type="select" label="Gap model" help="Gap[N] treatment">
                <option value="1" selected="true">CRE (regional error)</option>
                <option value="2">CSE (structural error)</option>
            </param>
            <param argument="--break" type="boolean" checked="false" truevalue="--break T" falsevalue="" label="Break chimeric fragments" help="Detect and break chimeric contigs at conflict breakpoints"/>
            <param argument="--map" type="select" label="Mapping preset" help="Ignored if .bam provided">
                <option value="map-hifi" selected="true">PacBio HiFi</option>
                <option value="map-pb" >PacBio CLR</option>
                <option value="map-ont">Nanopore</option>
            </param>
            <param argument="--mapq" type="integer" min="0" max="60" value="20" label="Minimum mapping quality" help="Minimum read mapping quality threshold"/>
            <param argument="--norm_window" type="float" min="0.0" max="1.0" value="0.0001" label="Normalization window fraction" help="Fraction of the total assembly length used as the window size for normalizing error counts"/>
            <param argument="--regional_window" type="integer" min="1" value="500000" label="Regional quality window size (bp)" help="Window size in base pairs for regional quality benchmarking across the assembly"/>
            <param argument="--plot" type="boolean" checked="false" truevalue="--plot T" falsevalue="" label="Generate plots" help="Create CRAQ visualization plots"/>
            <param argument="--plot_ids" type="data" format="tabular,txt" optional="true" label="Selected assembly IDs for plotting" help="File listing specific assembly IDs to plot (default: all IDs)"/>
            <param name="advanced_output" type="boolean" checked="false" label="Output advanced error region files" help="Output detailed CRE/CRH and CSE/CSH BED files for regional and structural error regions"/>
        </section>
    </inputs>
    <outputs>
        <collection name="runAQI_out" type="list" label="${tool.name} on ${on_string}: AQI Results">
            <discover_datasets pattern="__designation_and_ext__" directory="outputs/runAQI_out"/>
        </collection>
        <collection name="sr_out" type="list" label="${tool.name} on ${on_string}: Short Reads outputs">
            <discover_datasets pattern="__designation_and_ext__" directory="outputs/SRout"/>
            <filter>ngs_input</filter>
        </collection>
        <collection name="lr_out" type="list" label="${tool.name} on ${on_string}: Long Reads outputs">
            <discover_datasets pattern="__designation_and_ext__" directory="outputs/LRout"/>
            <filter>sms_input</filter>
        </collection>
        <collection name="regional_errors" type="list" label="${tool.name} on ${on_string}: Regional Error Regions">
            <discover_datasets pattern="__designation_and_ext__" directory="outputs/runAQI_out/locER_out"/>
            <filter>other_params['advanced_output']</filter>
        </collection>
        <collection name="structural_errors" type="list" label="${tool.name} on ${on_string}: Structural Error Regions">
            <discover_datasets pattern="__designation_and_ext__" directory="outputs/runAQI_out/strER_out"/>
            <filter>other_params['advanced_output']</filter>
        </collection>
    </outputs>
    <tests>
        <!-- Test 1:  Genome + SMS BAM Input, no NGS input -->
        <test expect_num_outputs="2">
            <param name="genome" location="https://zenodo.org/records/19091739/files/genome.fa"/>
            <param name="sms_input" location="https://zenodo.org/records/19091739/files/SMS_sort.bam"/>
            <output_collection name="runAQI_out" type="list" count="3"/>
            <output_collection name="lr_out" type="list" count="10"/>
        </test>
        <!-- Test 2: Genome + NGS BAM Input, no SMS input -->
        <test expect_num_outputs="2">
            <param name="genome" location="https://zenodo.org/records/19091739/files/genome.fa"/>
            <param name="ngs_input" location="https://zenodo.org/records/19091739/files/NGS_sort.bam"/>
            <section name="other_params">
                <param name="plot" value="true"/>
            </section>
            <output_collection name="runAQI_out" type="list" count="4"/>
            <output_collection name="sr_out" type="list" count="11"/>
        </test>
        <!-- Test 3: NGS FASTQ pair + break + snv variants + MAPQ30 -->
        <test expect_num_outputs="3">
            <param name="genome" location="https://zenodo.org/records/19091739/files/genome.fa"/>
            <param name="ngs_input" location="https://zenodo.org/records/19091739/files/NGS_R1.fq.gz,https://zenodo.org/records/19091739/files/NGS_R2.fq.gz"/>
            <param name="sms_input" location="https://zenodo.org/records/19091739/files/SMS_sort.bam"/>
            <section name="other_params">
                <param name="break" value="true"/>
                <param name="snv" value="true"/>
                <param name="mapq" value="30"/>
            </section>
            <output_collection name="runAQI_out" type="list" count="4"/>
            <output_collection name="sr_out" type="list" count="9"/>
        </test>
        <!-- Test 4: Genome + NGS Paired FASTQ + SMS BAM + Advanced outputs-->
        <test expect_num_outputs="5">
            <param name="genome" location="https://zenodo.org/records/19091739/files/genome.fa"/>
            <param name="ngs_input" location="https://zenodo.org/records/19091739/files/NGS_R1.fq.gz,https://zenodo.org/records/19091739/files/NGS_R2.fq.gz"/>
            <param name="sms_input" location="https://zenodo.org/records/19091739/files/SMS_sort.bam"/>
            <section name="other_params">
                <param name="advanced_output" value="true"/>
            </section>
            <output_collection name="runAQI_out" type="list" count="3"/>
            <output_collection name="lr_out" type="list" count="10"/>
            <output_collection name="sr_out" type="list" count="9"/>
            <output_collection name="regional_errors" type="list" count="5"/>
            <output_collection name="structural_errors" type="list" count="6"/>
        </test>
        <!-- Test 5: Plot + file ids selected for plotting -->
        <test expect_num_outputs="2">
            <param name="genome" location="https://zenodo.org/records/19091739/files/genome.fa"/>
            <param name="ngs_input" location="https://zenodo.org/records/19091739/files/SMS_sort.bam"/>
            <section name="other_params">
                <param name="plot" value="true"/>
                <param name="plot_ids" value="ids.txt"/>
            </section>
            <output_collection name="runAQI_out" type="list" count="4"/>
            <output_collection name="sr_out" type="list" count="11"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does?**

CRAQ (Clipping Reveals Assembly Quality) is a reference-free genome assembly quality evaluator.
It identifies potential errors in assembled sequences by analysing how reads clip (fail to align continuously)
at specific positions - without requiring a reference genome.

CRAQ produces two key quality scores:

- **R-AQI** (Regional Assembly Quality Index): captures small-scale errors such as indels and local misassemblies detected by short reads
- **S-AQI** (Structural Assembly Quality Index): captures large-scale structural errors such as chimeric joins and inversions detected by long reads

-----

**Inputs**

+---------------------------+----------+----------------------------------------------------------+
| Input                     | Required | Description                                              |
+===========================+==========+==========================================================+
| Assembly FASTA            | Yes      | Genome assembly to evaluate in FASTA format              |
+---------------------------+----------+----------------------------------------------------------+
| SMS long-read data        | No*      | PacBio or Nanopore data as BAM (sorted or unsorted)      |
|                           |          | OR one or more FASTQ/FASTQ.GZ sequence files             |
+---------------------------+----------+----------------------------------------------------------+
| NGS short-read data       | No*      | Illumina data as BAM (sorted or unsorted)                |
|                           |          | OR one or more FASTQ/FASTQ.GZ sequence files             |
+---------------------------+----------+----------------------------------------------------------+

\* At least one of SMS or NGS input must be provided. Using both together gives the most complete assessment.

.. class:: warningmark

If providing sequence files (FASTQ) rather than alignments, CRAQ will perform the mapping internally
using minimap2 for SMS and BWA for NGS. Ensure the correct mapping preset is selected under
**Other Parameters** when using raw reads.

-----

**Outputs**

**1) AQI Results** *(always produced)*

The primary output collection containing:

- ``AQI_summary.txt`` - final R-AQI and S-AQI scores summarising overall assembly quality
- ``regional_statistics.txt`` - per-region breakdown of error counts and coverage
- ``circos_plot.pdf`` - visualisation of quality metrics across the assembly *(only if plotting is enabled)*

**2) Long Read Outputs** *(produced when SMS input is provided)*

- Filtered long-read alignment in BAM format with index
- Putative structural error (CSE) breakpoint coordinates
- Heterozygous variant (CSH) breakpoint coordinates flagged by long reads

**3) Short Read Outputs** *(produced when NGS input is provided)*

- Filtered short-read alignment in BAM format with index
- Putative regional error (CRE) coordinates flagged by short reads
- Heterozygous variant (CRH) coordinates from short-read clipping patterns

**4) Regional Error Regions** *(advanced output, optional)*

BED files with precise coordinates of:

- CRE (Clipping-based Regional Errors): local assembly errors detected by short reads
- CRH (Clipping-based Regional Heterozygous variants): heterozygous positions in regional context

**5) Structural Error Regions** *(advanced output, optional)*

BED files with precise coordinates of:

- CSE (Clipping-based Structural Errors): large-scale misassemblies detected by long reads
- CSH (Clipping-based Structural Heterozygous variants): heterozygous structural positions
- Low-coverage regions and ambiguous breakpoints

-----

**Interpreting AQI Scores**

Both R-AQI and S-AQI are scored from 0 to 100, where higher is better:

+------------+-------------------+------------------------------------------+
| Score      | Quality           | Interpretation                           |
+============+===================+==========================================+
| 90 – 100   | Excellent         | Very few errors, high-confidence assembly|
+------------+-------------------+------------------------------------------+
| 70 – 89    | Good              | Minor errors, suitable for most analyses |
+------------+-------------------+------------------------------------------+
| 50 – 69    | Moderate          | Noticeable errors, use with caution      |
+------------+-------------------+------------------------------------------+
| < 50       | Poor              | Significant errors, reassembly advised   |
+------------+-------------------+------------------------------------------+

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