Mercurial > repos > iuc > craq
changeset 0:7895d95c01fa draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/craq commit fe19727db664bcad91b66546149cbf34a6a012e7
| author | iuc |
|---|---|
| date | Wed, 18 Mar 2026 13:17:03 +0000 |
| parents | |
| children | |
| files | craq.xml macros.xml test-data/ids.txt |
| diffstat | 3 files changed, 323 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/craq.xml Wed Mar 18 13:17:03 2026 +0000 @@ -0,0 +1,300 @@ +<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> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 18 13:17:03 2026 +0000 @@ -0,0 +1,22 @@ +<macros> + <token name="@TOOL_VERSION@">1.10</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">25.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">craq</requirement> + </requirements> + </xml> + <xml name="creators"> + <creator> + <person givenName="Ahmad" familyName="Mahagna" url="https://github.com/Smkingsize"/> + <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/> + <organization name="Galaxy Europe"/> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-023-42336-w</citation> + </citations> + </xml> +</macros> \ No newline at end of file