Mercurial > repos > iuc > map_damage
changeset 0:3db999d4e0c1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5
| author | iuc |
|---|---|
| date | Tue, 15 Jul 2025 19:00:59 +0000 |
| parents | |
| children | 761b6fdcac6e |
| files | map_damage.xml test-data/alignment.fa test-data/all_fasta.loc test-data/ref.fa test-data/ref.fa.fai test-data/reference_lgdistribution.txt test-data/reference_misincorporation.txt test-data/test_align.bam test-data/test_align.sam tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 12 files changed, 1684 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/map_damage.xml Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,555 @@ +<tool id="map_damage" name="mapDamage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> + + <description>Tracks and quantifies damage patterns in ancient DNA sequences</description> + + <macros> + <token name="@TOOL_VERSION@">2.2.2</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + + <xrefs> + <xref type="bio.tools">mapdamage</xref> + </xrefs> + + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mapdamage2</requirement> + </requirements> + + <version_command><![CDATA[mapDamage --version]]></version_command> + + <command detect_errors="aggressive"><![CDATA[ + + ln -s '$sbam_file' alignment.$sbam_file.ext && + + #if $reference.ref_source == 'history': + ln -s '$reference.history_reference' reference.fa && + #end if + + ## MAIN COMMAND LINE + + mapDamage + + ## INPUT / OUTPUT PARAMETERS + + --input alignment.$sbam_file.ext + + #if $reference.ref_source == 'builtin': + --reference '$reference.builtin_reference.fields.path' + #elif $reference.ref_source == 'history': + --reference reference.fa + #end if + + --folder 'mapDamage_results' + + ## GENERAL OPTIONS + + $merge_reference_sequences + + #if $downsampling.downsampling.downsampling_type != 'no_downsampling': + --downsample $downsampling.downsampling.downsample + #if $downsampling.downsampling.downsample_seed: + --downsample-seed $downsampling.downsampling.downsample_seed + #end if + #end if + + --length $window_size.length + --around $window_size.around + --min-basequal $min_basequal + $fasta + + ## GRAPHICS OPTIONS + + --ymax $graphics.ymax + --readplot $graphics.readplot + --refplot $graphics.refplot + + #if str($graphics.title): + --title '$graphics.title' + #end if + + $graphics.theme_bw + + ## STATISTICS OPTIONS + + #if $statistics.stats.no_stats: + $statistics.stats.no_stats + #else: + --rand $statistics.stats.rand + --burn $statistics.stats.burn + --adjust $statistics.stats.adjust + --iter $statistics.stats.iter + $statistics.stats.ends.ends_to_process + + #if not $statistics.stats.ends.ends_to_process: + $statistics.stats.ends.diff_hangs + #end if + + --seq-length $statistics.stats.seq_length + $statistics.stats.var_disp + $statistics.stats.mutation_model + $statistics.stats.nick_vector + #end if + + ## RESCALING OPTIONS + + #if $rescale.rescaling.rescale: + --rescale + #if $rescale.rescaling.rescale_length_5p: + --rescale-length-5p $rescale.rescaling.rescale_length_5p + #end if + #if $rescale.rescaling.rescale_length_3p: + --rescale-length-3p $rescale.rescaling.rescale_length_3p + #end if + #end if + + ]]></command> + + <inputs> + + <!--INPUT FILES--> + + <param name="sbam_file" argument="--input" type="data" format="sam,bam" label="SAM / BAM input file of aligned reads to be analyzed." help="Must contain a valid header."/> + + <conditional name="reference"> + <param name="ref_source" type="select" label="Use a built-in FASTA reference or retrieve one from your history?"> + <option value="builtin" selected="true">Built-in reference FASTA file</option> + <option value="history">From your history</option> + </param> + <when value="builtin"> + <param name="builtin_reference" type="select" label="FASTA genome to use as a reference in order to assess DNA damage" help="Contact your Galaxy team in order to add a reference"> + <options from_data_table="all_fasta"></options> + <validator type="no_options" message="No FASTA references are available, please contact your Galaxy administrators."/> + </param> + </when> + <when value="history"> + <param name="history_reference" type="data" format="fasta" label="FASTA genome to use as a reference in order to use DNA damage"/> + </when> + </conditional> + + <!--GENERAL OPTIONS--> + + <param argument="--merge-reference-sequences" type="boolean" truevalue="--merge-reference-sequences" falsevalue="" label="Merge reference sequences in result files?" help="Useful for memory usage."/> + + <param argument="--min-basequal" type="integer" min="0" max="93" value="0" label="Minimum PHRED score for base to be considered" help="(assumes PHRED+33 score)"/> + + <param argument="--fasta" type="boolean" checked="false" truevalue="--fasta" falsevalue="" label="Output alignments in FASTA format?"/> + + <section name="downsampling" title="Downsampling"> + <conditional name="downsampling"> + <param name="downsampling_type" type="select" label="Type of downsampling" help="Downsample using a percentage or a number of reads?"> + <option value="no_downsampling" selected="true">No downsampling</option> + <option value="p">Percentage of reads</option> + <option value="n">Number of reads</option> + </param> + <when value="no_downsampling"/> + <when value="p"> + <param argument="--downsample" type="float" min="0" max="1" label="Percentage of reads to sample" help="Must be between 0 and 1 (0 and 1 not included)"> + <validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="true" message="Percentage of reads to downsample must be > 0 and < 1"/> + </param> + <param argument="--downsample-seed" type="integer" optional="true" label="Downsampling seed" help="Seed (integer) used to randomly select reads for downsampling. Useful for reproducibility."/> + </when> + <when value="n"> + <param argument="--downsample" type="integer" min="1" label="Number of reads to sample" help="Must be superior or equal to 1"/> + <param argument="--downsample-seed" type="integer" optional="true" label="Downsampling seed" help="Seed (integer) used to randomly select reads for downsampling. Useful for reproducibility."/> + </when> + </conditional> + + </section> + + <section name="window_size" title="Analysis Window Size"> + <param argument="--length" type="integer" min="1" value="70" label="Number of nucleotides to process, starting from 5p and 3p end of read" help="(Bases which are located further than this from one of the two read ends will not be analyzed)"/> + <param argument="--around" type="integer" min="0" value="10" label="Number of nucleotides to retrieve before and after read" help="(This is used in order to look at purine enrichment before strand breaks)"/> + </section> + + <!--GRAPHICS OPTIONS--> + + <section name="graphics" title="Graphics Options"> + <param argument="--ymax" type="float" min="0" max="1" value="0.3" label="Graphical y-axis limit for nucleotide misincorporation frequency" help="(Bottom plot in the Fragmisincorporation_plot.pdf file)"> + <validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="false" message="--ymax must be > 0 and <= 1"/> + </param> + <param argument="--readplot" type="integer" min="0" value="25" label="Number of bases to plot from 5p and 3p ends (x-axis)" help="(Bottom plot in the Fragmisincorporation_plot.pdf file) // Must be inferior or equal to --length !"> + <validator type="in_range" min="0" exclude_min="true" message="--readplot must be > 0"/> + </param> + <param argument="--refplot" type="integer" min="0" value="10" label="Number of upstream and downstream nucleotides to plot for the composition plots" help="(Top four plots in the Fragmisincorporation_plot.pdf file) // Must be inferior or equal to --around !"/> + <param argument="--title" type="text" optional="true" label="Plot title" help="Title to give to the plots in the pdf files"/> + <param argument="--theme-bw" type="select" label="Graphical theme to use for the posterior prediction plot"> + <option value="" selected="true">gray (default)</option> + <option value="--theme-bw">bw (--theme-bw)</option> + </param> + </section> + + <!--STATISTICS OPTIONS--> + + <section name="statistics" title="Statistical Estimation Options"> + <conditional name="stats"> + <param argument="--no-stats" type="select" label="Enable statistical estimations?"> + <option value="" selected="true">Yes</option> + <option value="--no-stats">No</option> + </param> + <when value=""> + <param argument="--rand" type="integer" min="0" value="30" label="Number of random starting points for the likelihood optimization"/> + <param argument="--burn" type="integer" min="0" value="10000" label="Number of burn-in iterations"/> + <param argument="--adjust" type="integer" min="0" value="10" label="Number of adjust proposal variance parameter iterations"/> + <param argument="--iter" type="integer" min="0" value="50000" label="Number of final MCMC iterations"/> + <conditional name="ends"> + <param name="ends_to_process" type="select" label="Read ends to analyze for statistical estimation" help="(relates to --forward and --reverse options, default is to use both ends)"> + <option value="" selected="true">5p and 3p ends</option> + <option value="--forward">5p ends only</option> + <option value="--reverse">3p ends only</option> + </param> + <when value=""> + <param argument="--diff-hangs" type="boolean" checked="false" truevalue="--diff-hangs" falsevalue="" label="Overhangs are different in 5p and 3p?"/> + </when> + <when value="--forward"/> + <when value="--reverse"/> + </conditional> + <param argument="--seq-length" type="integer" min="1" value="12" label="Number of nucleotides (on both ends if both are used) to use for statistical estimations." help="Must be inferior or equal to the --length option !"/> + <param argument="--var-disp" type="boolean" checked="false" truevalue="--var-disp" falsevalue="" label="Variable dispersion in the overhangs?"/> + <param name="mutation_model" type="select" label="Substitution model to use in statistical estimation"> + <option value="" selected="true">HKY85 model (Hasegawa, Kishino and Yano, default option)</option> + <option value="--jukes-cantor">Jukes-Cantor model (--jukes-cantor)</option> + </param> + <param name="nick_vector" type="select" label="Calculation of the nick vector" help="Default option is to estimate nick frequencies along the sequence using a GAM (Generalized Additive Model), followed by smoothing. GAM estimation will only be done if there are enough substitutions."> + <option value="" selected="true">Estimate using a GAM + smoothing</option> + <option value="--use-raw-nick-freq">Estimate using a GAM, no smoothing (--use-raw-nick-freq)</option> + <option value="--fix-nicks">Make it constant (--fix-nicks)</option> + <option value="--single-stranded">Single-stranded library protocol (makes the vector constant by filling with ones) (--single-stranded)</option> + </param> + </when> + <when value="--no-stats"/> + </conditional> + </section> + + <!--RESCALING OPTIONS--> + + <section name="rescale" title="Rescaling options"> + <conditional name="rescaling"> + <param argument="--rescale" type="select" label="Perform rescaling of base quality according to DNA damage level?" help="This is helpful for downstream analyses, as damaged bases create less noise."> + <option value="" selected="true">No</option> + <option value="--rescale">Yes</option> + </param> + <when value="--rescale"> + <param argument="--rescale-length-5p" type="integer" min="0" optional="true" label="Number of bases to rescale at the 5p end" help="defaults to --seq-length if left empty. // Must be inferior or equal to --seq-length !"/> + <param argument="--rescale-length-3p" type="integer" min="0" optional="true" label="Number of bases to rescale at the 3p end" help="defaults to --seq-length if left empty. // Must be inferior or equal to --seq-length !"/> + </when> + <when value=""/> + </conditional> + </section> + + </inputs> + + <outputs> + + <!--RUNTIME LOG FILE--> + + <data name="runtime_log" format="txt" from_work_dir="mapDamage_results/Runtime_log.txt" label="${tool.name} on ${on_string}: Runtime_log.txt"/> + + <!--RESULT FILES THAT DESCRIBE DNA DAMAGE OBSERVED ON READS--> + + <collection name="damage_visualisation" type="list" label="${tool.name} on ${on_string}: Data description files and plots"> + <data name="dnacomp" format="txt" from_work_dir="mapDamage_results/dnacomp.txt" label="${tool.name} on ${on_string}: dnacomp.txt"/> + <data name="misincorporation" format="txt" from_work_dir="mapDamage_results/misincorporation.txt" label="${tool.name} on ${on_string}: misincorporation.txt"/> + <data name="5pCtoT_freq" format="txt" from_work_dir="mapDamage_results/5pCtoT_freq.txt" label="${tool.name} on ${on_string}: 5pCtoT_freq.txt"/> + <data name="3pGtoA_freq" format="txt" from_work_dir="mapDamage_results/3pGtoA_freq.txt" label="${tool.name} on ${on_string}: 3pGtoA_freq.txt"/> + <data name="Fragmisincorporation_plot" format="pdf" from_work_dir="mapDamage_results/Fragmisincorporation_plot.pdf" label="${tool.name} on ${on_string}: Fragmisincorporation_plot.pdf"/> + <data name="lgdistribution" format="txt" from_work_dir="mapDamage_results/lgdistribution.txt" label="${tool.name} on ${on_string}: lgdistribution.txt"/> + <data name="Length_plot" format="pdf" from_work_dir="mapDamage_results/Length_plot.pdf" label="${tool.name} on ${on_string}: Length_plot.pdf"/> + </collection> + + <!--RESULT FILES THAT DESCRIBE STATISTICAL ESTIMATIONS OF DAMAGE PARAMETERS--> + + <collection name="statistical_estimation" type="list" label="${tool.name} on ${on_string}: Statistical estimation files and plots"> + <data name="dnacomp_genome" format="csv" from_work_dir="mapDamage_results/dnacomp_genome.csv" label="${tool.name} on ${on_string}: dnacomp_genome.csv"/> + <data name="Stats_out_MCMC_iter_summ_stat" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter_summ_stat.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter_summ_stat.csv"/> + <data name="Stats_out_MCMC_hist" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_hist.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_hist.pdf"/> + <data name="Stats_out_MCMC_iter" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter.csv"/> + <data name="Stats_out_MCMC_trace" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_trace.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_trace.pdf"/> + <data name="Stats_out_MCMC_correct_prob" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_correct_prob.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_correct_prob.csv"/> + <data name="Stats_out_MCMC_post_pred" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_post_pred.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_post_pred.pdf"/> + <filter>statistics['stats']['no_stats'] == ''</filter> + </collection> + + <!--OPTIONAL ALIGNMENT OUTPUT FILES--> + + <data name="rescaled_bam" format="bam" from_work_dir="mapDamage_results/alignment.rescaled.bam" label="${tool.name} on ${on_string}: Rescaled .bam file"> + <filter>rescale['rescaling']['rescale'] == '--rescale'</filter> + </data> + + <data name="fasta_alignment" format="fasta" from_work_dir="mapDamage_results/alignment.fasta" label="${tool.name} on ${on_string}: FASTA file of alignments"> + <filter>fasta</filter> + </data> + + </outputs> + + <tests> + + <!--GENERAL TESTS--> + <!--NB: only data_visualisation files are tested, as the statistical estimation process is stochastic and files will always be different--> + + <!--SAM input--> + <test expect_num_outputs="17" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.sam" ftype="sam"/> + <conditional name="reference"> + <param name="ref_source" value="history"/> + <param name="history_reference" value="ref.fa" ftype="fasta"/> + </conditional> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + </test> + + <!--BAM input--> + <test expect_num_outputs="17" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.bam" ftype="bam"/> + <conditional name="reference"> + <param name="ref_source" value="history"/> + <param name="history_reference" value="ref.fa" ftype="fasta"/> + </conditional> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + + </test> + + <!--TEST TO VERIFY BUILT-IN REFERENCE GENOMES WORK AS INTENDED--> + <test expect_num_outputs="9" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.bam" ftype="bam"/> + <conditional name="reference"> + <param name="ref_source" value="builtin"/> + <param name="builtin_reference" value="test"/> + </conditional> + <section name="statistics"> + <conditional name="stats"> + <param name="no_stats" value="--no-stats"/> + </conditional> + </section> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + </test> + + <!--TEST TO VERIFY no_stats OPTION WORKS AS INTENDED--> + <test expect_num_outputs="9" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.sam" ftype="sam"/> + <conditional name="reference"> + <param name="ref_source" value="history"/> + <param name="history_reference" value="ref.fa" ftype="fasta"/> + </conditional> + <section name="statistics"> + <conditional name="stats"> + <param name="no_stats" value="--no-stats"/> + </conditional> + </section> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + </test> + + <!--TEST TO VERIFY fasta OPTION WORKS AS INTENDED--> + + <test expect_num_outputs="10" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.sam" ftype="sam"/> + <conditional name="reference"> + <param name="ref_source" value="history"/> + <param name="history_reference" value="ref.fa" ftype="fasta"/> + </conditional> + <section name="statistics"> + <conditional name="stats"> + <param name="no_stats" value="--no-stats"/> + </conditional> + </section> + <param name="fasta" value="true"/> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + <output name="fasta_alignment" file="alignment.fa" compare="diff" count="1"/> + + </test> + + <!--TEST TO VERIFY rescale OPTION WORKS AS INTENDED--> + <!--BAM file is not compared, as it depends on the stochastic statistical estimations, and may therefore differ (though perhaps not with this dataset)--> + <test expect_num_outputs="18" expect_exit_code="0"> + + <param name="sbam_file" value="test_align.sam" ftype="sam"/> + <conditional name="reference"> + <param name="ref_source" value="history"/> + <param name="history_reference" value="ref.fa" ftype="fasta"/> + </conditional> + <section name="rescale"> + <conditional name="rescaling"> + <param name="rescale" value="--rescale"/> + </conditional> + </section> + + <output_collection name="damage_visualisation" type="list"> + <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/> + <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/> + </output_collection> + + </test> + + </tests> + + <help><![CDATA[ + **Overview**: + +mapDamage is a computational framework which allows for authentication of ancient DNA NGS reads by tracking and quantifying damage patterns which are specific to ancient DNA molecules. + +The following damage patterns can be studied thanks to mapDamage's plots and Bayesian statistical estimations: + + * Fragment length + * Purine enrichment before strand breaks + * Cytosine deaminations and resulting misincorporations (C → T and G → A) (in single-stranded and double-stranded context) + * Nicking + * Overhang lengths + +This help is divided into subsections: Inputs, Outputs, Parameters, and General Usage. For a quick read, jump down to the 'General Usage' section! + +----- + + **Inputs**: + +mapDamage only needs two input files: + + * An alignment map file, either in BAM or SAM format. + + * A reference sequence, in FASTA format. Can either be uploaded to Galaxy or chosen from a list of built-in references (no uploading required). + +----- + + **Outputs**: + +The most commonly used outputs are listed in the 'General Usage' section below. + +mapDamage has plenty of output files, which have been grouped into Data Collections in order to improve clarity. + +* **Runtime_log.txt**: Contains general information about the command line which was executed by Galaxy, as well as the time taken by each task. + +* Outputs in the **'Damage Visualisation' collection**: These outputs (text files and associated PDF plots) describe the damage patterns observed in your input BAM / SAM. No statistical estimations were involved in their generation. + + - **dnacomp.txt**: Contains the counts of each base (ATGC) across all reads, for the first X bases from the end in question (X is given by --length option) as well as the Y bases surrounding the end in question (Y is given by the --around option). This is broken down by end (3p/5p) and by strand (+/-), and by chromosome/contig. + + - **misincorporation.txt**: Contains the counts of each type of mutation (substitutions, deletions, insertions, soft-clipping) across all reads, for the first X bases from the end in question (X is given by the --length option). This is broken down by end (3p/5p), by strand (+/-), and by chromosome/contig. + + - **3pGtoA_freq.txt**: Contains the frequencies of G → A substitutions across all reads, for the first N bases from the 3p end (N is given by --readplot). + + - **5pCtoT_freq.txt**: Contains the frequencies of C → T substitutions across all reads, for the first N bases from the 5p end (N is given by --readplot). + + - **Fragmisincorporation_plot.pdf**: Contains plots of the above data: One frequency plot per nucleotide, as well as a plot describing the distribution of C → T and G → A substitutions + + - **lgdistribution.txt**: Contains the distribution of reads according to strand on which they map (+/-) and length. + + - **Length_plot.pdf**: Contains plots of the above data. + +* Outputs in the **'Statistical Estimations' collection**: These outputs describe the Bayesian statistical estimation process as well as its results. + + - **dnacomp_genome.csv**: Contains whole-genome base frequencies, as calculated by seqtk. + + - **Stats_out_MCMC_iter_summ_stat.csv**: Contains mean value, standard deviation, acceptance ratio and posterior distribution for the following parameters: + + * θ : difference rate between reference and sample that is not due to DNA damage. + * ρ : transversion / transition bias. + * δd : rate of Cytosine deamination in a double-stranded context. + * δs : rate of Cytosine deamination in a single-stranded context. + * λ : probability of terminating an overhang. + * The model's log-likelihood. + + - **Stats_out_MCMC_hist.pdf**: Contains plots of the posterior distribution of the 6 parameters described above. + + - **Stats_out_MCMC_iter.csv**: Contains the mean values for each of the 6 parameters described above at every MCMC iteration. + + - **Stats_out_MCMC_trace.pdf**: Contains trace plots derived from the previous file. + + - **Stats_out_MCMC_correct_prob.csv**: Contains posterior probabilities that C → T and G → A substitutions are due to DNA damage, for the first N bases from both 3p and 5p ends (N is given by --seq-length) + + - **Stats_out_MCMC_post_pred.pdf**: Contains plots derived from the previous file, as well as predictive intervals for these probabilities. + + + +* **alignment.fasta** (if --fasta option was set): FASTA file containing alignments as specified by the BAM / SAM file. FASTA file also contains the nucleotides surrounding the reads as defined by the --around parameter. + +* **alignment.rescaled.bam** (if --rescale option was set): BAM file containing a rescaled version of the alignment: the --rescale parameter leads to a re-evaluation of base quality based on misincorporation probability, which can decrease the noise created by these misincorporations in downstream analyses. + +----- + + **Options**: + +mapDamage has many parameters, which have been grouped into sections for convenience. + +Here, the objective is to provide a guide on the most important tool features, and only a few key parameters are therefore detailed. + +More details concerning each option can be found: + + - on the mapDamage GitHub. + - in the descriptions given below the options. + +Some options may lack a detailed explanation (statistics related options in particular). In this case, please refer to the citations below and / or to the source code, available on the mapDamage GitHub. + + * **--no-stats**: Do not perform statistical estimation of damage parameters. This can be very useful if you only plan on looking at the *Fragmisincorporation.pdf* plot in order to see if the damage patterns are present, as it tends to vastly improve the run-time. + * **--rescale**: Produces a new BAM alignment file where base qualities have been re-evaluated according to damage probability. Please note that this can only be done if statistical estimations are performed. Useful for reducing noise in downstream analyses: aDNA related misincorporations (C → T, G → A) are no longer falsely flagged as SNPs. + * **--merge-reference-sequence**: Merges results for the different sequences (chromosomes or contigs) in your reference FASTA file. Instead of one table per reference sequence in the dnacomp.txt and misincorporation.txt files, there is one table describing every sequence. This greatly reduces the size of these files (size is more or less divided by the number of reference sequences) + + * Options regarding **specific library preparation protocols**: By default, mapDamage assumes that you are working with merged paired-end reads, from a double-stranded library protocol. If that is not the case, the tool authors have made recommendations, which you can check out in the supplementary data of Jónsson et al. (2013). + + - For **single-stranded libraries**: + + * Calculation of the nick vector: single-stranded library protocol (**--single-stranded**). The authors recommend this option for treating single-stranded library data, and remark that the user should see elevated C → T substitution frequencies at both ends in the Stats_out_MCMC_post_pred.pdf plot. + + - For **single-end libraries**: + + * Read ends to analyze for statistical estimation: 5p ends only (**--forward**). This forces mapDamage to only analyze the 5p ends of reads. + * Overhangs are different in 5p and 3p?: Yes (**--diff-hangs**). This option allows different mean lengths for the two overhangs, which can be another way to account for single-end data. + +----- + + **General usage**: + + (This description is also based on the supplementary data of Jónsson et al. (2013)) + + **Launching mapDamage** + + For a simple usage of mapDamage, the user only needs to provide the two input files (alignment file and reference file), and press the 'Run tool' button. + + If downstream SNP analyses are in order, then one may want to use the rescaling feature, which will reduce the noise induced by cytosine deamination in these analyses. + + Statistical estimation may be disabled to improve run-time, if the user doesn't intend to make use of it. + + **Analyzing the outputs** + + The first outputs one should have a look at are the *Fragmisincorporation_plot.pdf* and the *Length_plot.pdf* files. One can check if the expected damage is present, and if there are any problems with the dataset. + + If statistical estimations were run, the user should check if the proposed model is a good fit: do the empirical substitution frequencies (*Fragmisincorporation.pdf* plot) fall within the prediction intervals (*Stats_out_MCMC_post_pred.pdf* plot) ? + + The fit can also be assessed by looking at the *Stats_out_MCMC_trace.pdf* plot, to check if an equilibrium was reached over the course of the iterations. Finally, one can have a look at the acceptance ratio values in the *Stats_out_MCMC_iter_summ_stat.csv* file (3rd row), which should be between 0.1 and 0.3. + + If the fit is not correct, it may be improved by increasing the values of the --rand, --burn, --adjust and --iter options. + + If the fit looks correct, the rescaled BAM file can be confidently used, and the values of the damage parameters described in the *Stats_out_MCMC_iter_summ_stat.csv* may be used for comparison across samples. + ]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btt193</citation> + <citation type="doi">10.1093/bioinformatics/btr347</citation> + </citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment.fa Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,80 @@ +>minc:123214052 +AGAAAAAGGA +>minc:123214052:414-495 +TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTGTTGTCTTT +>simulated_read_1_+ +TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTATTGTCTTT +>minc:123214052 +AGTAAGGTCC +>minc:123214052 +TGAGAAGATT +>minc:123214052:1173-1233 +ACTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAGCGT +>simulated_read_2_+ +ATTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAACAT +>minc:123214052 +GGAATGAATG +>minc:123214052 +GAGGGAAGAT +>minc:123214052:3161-3236 +TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACGGAC +>simulated_read_3_+ +TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACAGAC +>minc:123214052 +AGAGAGCGGA +>minc:123224581 +GGGAGAGAAT +>minc:123224581:211-282 +TTGCAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC +>simulated_read_4_+ +TTGTAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC +>minc:123224581 +AAGGTCCAGT +>minc:123224581 +AGAAAAGGGT +>minc:123224581:397-472 +TTTTCAGTGAGCAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATGGATCTTTATATTGTATCT +>simulated_read_5_+ +TTTTTAGTGAGTAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATAGATCTTTATATTGTATCT +>minc:123224581 +CATGGAAGGG +>minc:123224581 +AAGAGCTGGG +>minc:123224581:765-825 +TTCTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTGTTGGCACC +>simulated_read_6_+ +TTTTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTATTGACACC +>minc:123224581 +AGAAGGGGGA +>minc:123224581 +GAAGATAGGT +>minc:123224581:1277-1351 +TATTAGTTGTGCAGTCTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC +>simulated_read_7_+ +TATTAGTTGTGCAGTTTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC +>minc:123224581 +AGAATTGGCC +>minc:123230223 +CAGAAGGAGA +>minc:123230223:288-341 +TATTGTGATACCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAGTC +>simulated_read_8_+ +TATTGTGATATCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAATC +>minc:123230223 +AAAGAAGAGC +>minc:123230223 +GAGGTGCAGA +>minc:123230223:822-880 +TTACTGCTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAGAAGCGTATGCTTGCTGTC +>simulated_read_9_+ +TTATTGTTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAAAAGCGTATGCTTACTATC +>minc:123230223 +GAAAGGGATG +>minc:123230223 +CTAAAACTGA +>minc:123230223:1017-1080 +CATTCCAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTGACACAT +>simulated_read_10_+ +TATTCTAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTAACACAT +>minc:123230223 +GAGATGAAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,1 @@ +test test_reference Reference file for planemo tests ${__HERE__}/ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,140 @@ +>minc:123214052 K14442 ATP-dependent RNA helicase DHX36 [EC:5.6.2.6] | (RefSeq) DExH-box ATP-dependent RNA helicase DExH5, mitochondrial (N) +atgccccttctctctccactttttcaaatccctcccaaactcatcatgaaggatcggcct +cccccgtcctacggcgccgtttacgttcctcctcaccaacgtctccgctcggtcatcgcc +agtcgcgcctcaattccttcgcttcctcacttaccagcactacaacaacaaaataataat +aatttcagtaataatcataataaaaatattaatgatgataataaaaagagactgaagtat +aactcaggttcagcgtacagtggagtatccgaggaaggctctgatcgggagctggatacg +tggctgctaccgggtgcttacccctctgataatgtggaggagtggagaaggaagttgact +gcgtttttatgtgacaagtcaaagcaagagttgatctcaagggagaaaaaggatagatgt +gattttgagcaactgtcagctctggctagtggcatgggtttgtatagtcatctgtacgca +aaagttgttgtctttagtaaggtcccactgccaaactacagatttgatttagatgatagg +cggccacagagggaggtgaccttatcccttgggttgctcagacgaattgattactatctt +ggagaatacttctctcaaaagtataggaataagggaagttttgtggatctatccgtctca +aggtctagcagtagtagtagtcttgctactgaagaaggtctttttgaacaaccagatcaa +tcagtatccagtaattctgtcatggataaaattttgcagcgacgaagtttacaactgcgt +gatcagcagcaagcttggcaggaatctccagatggtagaaaaatgcttgaatttcgaaga +agtctccctgcttataaggagaaggacgctattctgacagccatttcacaaaatcaggtc +ataattatatcaggtgaaactggctgtggcaagaccacacaaattcctcagttcatattt +gagtccgaaatagaatctgttcgtggagctgtttgtagtgttatttgtacacaaccaaga +agaatatctgcaatttctgtttctgagagagttgcttcagagagaggggagacattgggt +gaatctgttgggtataaagttcggctggagggcgtgaaagggaaggatacccatcttctc +ttctgcaccacaggcattttgttgagaagattactggttgatagaaatttgaaaggtgta +actcatgttattgttgatgagattcatgagcgtggaatgaatgaggattttctgcttatt +gtccttaaagatctcctccctcgccggcctgaattgaagctgattctgatgagtgcaaaa +ctagatgcagagctttttttgtcctactttggtggagctatgataattcacattccgggt +ttcacataccctgtcagaactcattttctggaaaatatattggaagtgacgggttacaga +ttgaccccatttaatcaaattgatgattatggcgaagaaaaaatgtggaaaatgagcaaa +caagcaccaagaaaaaggaagagccaaattgcatctttagttgaggatgcacttagagtg +gccaatttcaaggagtatagcccccagactaaggagtcattgtcatgttggaatcctgat +tgtattggttttaatctcattgaatacctcctatgtcatatttgtgagaaggaaagacct +ggtgctgttctagtctttatgactggttgggatgacataaattctcttaaggataaacta +caagctcatcctatattaggagattcaagccgagtattgttacttacctgccatggttct +atggctagttcagagcagagtttaatatttgacgagcctgaaggtggagtgaggaaaata +gtgcttactactaacatagctgagactagtatcaccattaatgatgttgtttttgtcatt +gactgtgggaaagcaaaggagacatcttatgatgcactgaataacacttcttgtctgctt +ccttcctggatttccaaggtttctgctcaacaaagaagaggaagggctggccgtgttcaa +ccaggagaatgttaccatctgtatcctaggtctgtgtatgatgcttttgcagaatatcag +cttcctgaaattttaaggacacctttgcagtctctatgcttgcaaattaaaagtttaaaa +cttgggagtatttctgagttcttatccagggctctgcagtcacctgagttgctagctgtc +caaaatgctattgaatatttaaaaatcactggggccttggaccagaatgaagacttgact +gtcttagggcggtacttgaccatgcttccaatggaacccaaacttggaaagatgctaata +ttaggtgccatcttcaaatgtctggaaccagtattaacaattgttgctggccttaatgtc +agagatcctttcttagcaccagtggacaaaaaggatcttgctgaggctgcaaagtctcag +ttttcctgtgatcatagtgaccatcttgcacttgtacgggcttacgagggatggaaagat +gctgaaagagaccttgctggatacgaatactgttggaaaaactttctctcatttcaatca +atgaaagctatcgattctcttcgggatgagttcttctctttgctcagggatactggtctt +gttgattgcaacacaaccatttgcaatgcatggagctatgatgatcatcttgttcgagca +gttatttgttatggtctttaccctggaatttgctccgttgtgaacaatgtgaagtccttt +tcactgaaaactatggaagacggccatgtgcttctatactctaattctatcaatgctcgg +caacctgaaattccatacccatggctggttttcaatgagaagataaaagtgaactctatt +tttctaagggattcaacagctatctgtgattcagtgttgctcctgtttggtggtagcatc +tctcaaggaaacactgatgggggacacttgaaaatgatgggaggatatttagaattcttc +atggaacctgcactttctgatatgtatcaatgtttaaggagagaacttgatgagctgatt +cagaataagttactcaatcccagaatggaaatgcacatgtatcgtgatctcctatctgca +gttcgattgcttgtttcagaagatcgttgcgagggaagatttgtatttggtcgccaggtg +cttaagtcgcttaagtcttcacctgtgccattacagccagctttgattccacggacagag +agcggacctgggggcgataatcctaagagtcagctccaaacattgctcaccagggcagga +tatgctgcccccagctacaaatcaagacaattgaagaacaaccagttcttggctacagtg +gagttcaatggaattcaaattatgggtcggccttgcaacaataagaagagcgcagagaag +gatgccgcagctgaggcactgcagtggctaatgggagggacccagacaagccttgaatgt +ataaatcaaatgtcactgttactgaagaaagcaagaaggatcacttctgaatcagcacca +ccctcaagttcatag +>minc:123224581 K20476 RAB6A-GEF complex partner protein 1 | (RefSeq) guanine nucleotide exchange factor subunit RIC1-like (N) +atgtacatgtcgtacggatggccacaggtgatcccaatagagcaagggcagtgttcgtcg +tctcaacggatcatatacttgaaagttatcaatggcttattactcgttgtctctccttca +catgtcgagctgtggagttcctcgcggcataaagtgaggttagggaaatataagagggat +tcagagtcgctgcagagagagggagagaatttgcaagctttgtggagccctgatggaaaa +ttgatcgctgtgattacgtcatctttttttcttcacattttcaaggtccagtttacagaa +aaaagaatacaaattggagcaaagcatccttctggtttgtttttggcaaatatatttctt +gttctcagtgagcaggtgccttttgcagaaaagggtttttcagtgagcaatattgtgagc +gataacaaacatatgctacttggactttctgatggatctttatattgtatctcatggaag +ggggagttctgtggagcttttgaactcaatgactttcgatatgatagcagctcagtgaca +ctactaccaaattccctgagtaatggctttgcttctgcagagacttcaggagcttttgtt +tctggtcacaaattctccagaaagtgcgctattgtccagctggagctttgctttctaatg +agactgcttcttattgtatattctgatggaaaactgatatcatgctctataagtaagaaa +ggtttaaagcaacctgaatttattaaagttgaaaaagagctgggttctggtgatgttgta +tgtgcttcagtggcggcagagcaacaaattgttgctgttggcaccagaagggggattgtt +gagctatatgacctggcagaatctgcatcactcattcgtactgtgtctttgtacgactgg +ggatactcaatggatgatactggttctgtcagttatattgcatggacacctgataattct +gcttttgctgttgggtggaagtcaagaggacttactgtgtggtctgtttcggggtgtcgt +ttgatgtcaacaatccgtcagattggcttaagttctgtgtcttctccagttgcaaagcca +aaccaagactttaaatatgagccactaatgagcggcacctctctggttcagtgggatgaa +tatggatataggctttacgcaattgaggaagaatcgtcagagcaaattcttgcattttcc +tttggcaaatgttgtattagcagaggagtatctggcatgacttatgcccgtcaagtaatt +tatggtgaagataggttattagttgtgcagtctgaagatactgatgaacttaagctttta +catttaaaccttccagtttcttatatctcccagaattggcctgtccaacatgtggcagct +agcaaggatggaatgtacttagcagttgctggtcttcatgggttaatattatatgatata +aggctgaaaaagtggcgagtatttggagatatcacgcaggaacaaaagattcagtgcaaa +ggtttgctgtggctgggaaagattattgttgtctgcaactacattgattcttctaacatg +tatgaactgcttttttatcctagatatcatcttgatcagagctcactactctgtcggaaa +cctttgcttgcaaaaccaatggtgatggatgtctaccaagattatatattggtgacctat +cgcccatttgatgtccacatattccatgtgaaattatttggtgaattgacaccttcaaac +actccagacctacaactttctacagtacgagaactttcaatcatgactgcgaagagccac +ccagctgctatgcgctttatccctgatcaggttactggtgaaagtacattaaacaatcga +gtttcatctgaagaagatttgtctgagagggagcctgcaagatgtttgatattaagagca +aatggggagctttcacttctggatttagatgatggaagggaaagggagcttaccgattct +gttgaattattttgggttacttgtggacaatcagaggagaagatgagtctaattgaggaa +gtttcatggttggattatggctttcgagggatgcaggtttggtatccgtcttcgggtgtt +gacccttttaagcaggaggactttttgcatttggacccggagttggagtttgaccgtgag +gtgtatcctttgggtcttcttccaaatgctggtattgttgttggcgtttcgcagagactg +tcgttttcagcatgcacagagtttccttgttttgaaccaactcctcaagcccaaactata +ttgcattgcctacttcggcatcttcttcagagggacaaaattgtggaggctttacggttg +gcacagttgtctgcagaaaagcctcatttttcacattgtctggagtggcttctttttact +gtatttgaagctgaaatttccaggcaaaatataaacaagaaccaaatctcaacccttaaa +cgtgctgccaacttttctcttttggagaagacttgcaatttaattagaaattttcctgag +taccttagtgttgttgtcagtgttgctagaaagactgatggtcgacattggtcagatttg +ttctctgctgctggaagatctacagagttgtttgaggactgcttccagcggagatggtat +cgcactgcggctggctatattcttgtgattgctaaacttgaaggtcccgctgtcagtcaa +tattgtgccttacgtttattacaggcaacacttgatgaatgtttatatgaacttgctggg +gaactggtgagattcttactgagatctggaagggaatttgaaccagcatcaactgattca +gaaaaattatcacccagattcttgggctattttctttttcctcctagttacaggaggtca +tctttggataaaagcacctctctcaaggagcagagtcctaatgttgcttctgttaagaac +atcttagaaaatcatgctagctatttgatgtcggggaaagaactttccaagcttgttgca +tttgtaaagggcactcagtttgatttagtggaatatcttcaacgagaaagatatggtagt +gctcgcttagagaattttgcttcagcgcttgaactgattgcgcaaaagcttcacatgggt +acactgcagagcaggttggatgcagaatttctcttggctcatatgtgctctgtcaagttc +aaagaatggatagttgtacttgccactcttttaagacgatctgagattctttttgatctt +ttctgtcatgatacacggttatggaaagcttatgccattacattacagtctcattccacg +ttcgccgagtaccaagatcttcttgaatccttggaggagagacttacatctgttttgaat +acagaagacaaatga +>minc:123230223 K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] | (RefSeq) alcohol dehydrogenase-like 7 (N) +atggatagcgacaatttgttaagggaaaccgcagggaagccgattcgatgcagagctgcc +atagctcgagtgccaggggagtctctggtaatagaggagattctagtggaccctccgagt +tcccatgaagttcggattcgaatcatctgtacaggtctctgtcacagcgatatcactttc +tggaaaatgaaggattttcctgctgttttcccaagaattctgggtcatgaggctattggg +aaggtggaaagtgtgggggagaatgtaaaagatgtagcagaaggagatattgtgatacca +tattttctggcagattgtagtgaatgtgtcgattgcaagtcaaagaagagcaacctatgt +tcaaaattccccttcaaggtctctccttggatggctagatctgagacaagcagattcaga +gatctcaagggacaaactttgcatcattttttatttgtttcaagttttagtgagtatact +gtggtagacattgctaatatagtaaagattgaccccgacgtccctccaagtaaggcatgc +ctcctaagttgtggggtatcaacaggggttggagctgcttggagaacagcaaacgtggag +gctggatcaactgttgtcatatttgggctaggatcaattggattagctgtcgcagaggga +gcaagactttgtggtgctactagaattataggtgtcgatgtgattccagagaaatttgaa +ataggaaaaaagtttggagtcacagaatttgttaatgctaaaagttgtggggataaatca +gtaagccaggtaatcaatgagatgactgatggaggtgcagattactgctttgagtgtgtt +ggttcttcatccttggtgcaagaagcgtatgcttgctgtcgaaagggatggggaaagaca +gttgtgttgggagtggacaagccaggagcacaggtgagcttaagctctcttgatgtcctt +gagagtggaaaaattctgaagggatcattgtttggaggactcaaagctaaaactgacatt +ccaattctgctgaaacgttacatggacaaggaattacaattagatgaatttgtgacacat +gagatgaagtttgaagagatcaataaagcctttgatttacttattcaaggaaagtgtcta +cggtgtgtcatttggatggacaaataa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa.fai Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,3 @@ +minc:123214052 3555 141 60 61 +minc:123224581 3375 3883 60 61 +minc:123230223 1167 7472 60 61
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_lgdistribution.txt Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,12 @@ +# table produced by mapDamage version 2.2.2 +# using mapped file test_align.bam and ref.fa as reference file +# Std: strand of reads +Std Length Occurences ++ 82 1 ++ 61 2 ++ 76 2 ++ 72 1 ++ 75 1 ++ 54 1 ++ 59 1 ++ 64 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_misincorporation.txt Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,844 @@ +# table produced by mapDamage version 2.2.2 +# using mapped file test_align.bam and ref.fa as reference file +# Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads +Chr End Std Pos A C G T Total G>A C>T A>G T>C A>C A>T C>G C>A T>G T>A G>C G>T A>- T>- C>- G>- ->A ->T ->C ->G S +minc:123214052 3p + 1 0 1 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 2 1 0 1 1 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 3 0 1 1 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 4 0 1 2 0 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 5 1 1 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 6 1 0 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +minc:123214052 3p + 7 0 1 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_align.sam Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,15 @@ +@HD VN:1.5 SO:unsorted GO:query +@SQ SN:minc:123214052 LN:3555 +@SQ SN:minc:123224581 LN:3375 +@SQ SN:minc:123230223 LN:1167 +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/home/taulagnon/miniconda3/envs/ancientDNA/bin/bowtie2-align-s --wrapper basic-0 -x index -S test_align.sam -U reads.fa" +simulated_read_1 0 minc:123214052 414 42 82M * 0 0 TAGATGTGATTTTGAGCAACTGTCAGCTCTGGCTAGTGGCATGGGTTTGTATAGTCATCTGTACGCAAAAGTTATTGTCTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGFGFFFCCCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:73G8 YT:Z:UU +simulated_read_2 0 minc:123214052 1173 23 61M * 0 0 ATTGGTTGATAGAAATTTGAAAGGTGTAACTCATGTTATTGTTGATGAGATTCATGAACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGFGG AS:i:-16 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C55G1G1 YT:Z:UU +simulated_read_3 0 minc:123214052 3161 42 76M * 0 0 TTGTATTTGGTCGCCAGGTGCTTAAGTCGCTTAAGTCTTCACCTGTGCCATTACAGCCAGCTTTGATTCCACAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFGFFCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:72G3 YT:Z:UU +simulated_read_4 0 minc:123224581 211 42 72M * 0 0 TTGTAAGCTTTGTGGAGCCCTGATGGAAAATTGATCGCTGTGATTACGTCATCTTTTTTTCTTCACATTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGFGFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:3C68 YT:Z:UU +simulated_read_5 0 minc:123224581 397 24 76M * 0 0 TTTTTAGTGAGTAATATTGTGAGCGATAACAAACATATGCTACTTGGACTTTCTGATAGATCTTTATATTGTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGFGCCCC AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:4C6C45G18 YT:Z:UU +simulated_read_6 0 minc:123224581 765 23 61M * 0 0 TTTTGGTGATGTTGTATGTGCTTCAGTGGCGGCAGAGCAACAAATTGTTGCTATTGACACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:2C49G3G4 YT:Z:UU +simulated_read_7 0 minc:123224581 1277 42 75M * 0 0 TATTAGTTGTGCAGTTTGAAGATACTGATGAACTTAAGCTTTTACATTTAAACCTTCCAGTTTCTTATATCTCCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGFGGFFGFFFCC AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15C59 YT:Z:UU +simulated_read_8 0 minc:123230223 288 24 54M * 0 0 TATTGTGATATCATATTTTCTGGCAGATTGTAGTGAATGTGTCGATTGCAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:10C40G2 YT:Z:UU +simulated_read_9 0 minc:123230223 822 0 59M * 0 0 TTATTGTTTTGAGTGTGTTGGTTCTTCATCCTTGGTGCAAAAAGCGTATGCTTACTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGFGF AS:i:-28 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:3C2C33G12G2G2 YT:Z:UU +simulated_read_10 0 minc:123230223 1017 23 64M * 0 0 TATTCTAATTCTGCTGAAACGTTACATGGACAAGGAATTACAATTAGATGAATTTGTAACACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGFFGFFFFFFFCCCCCCCCC AS:i:-17 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0C4C51G6 YT:Z:UU
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc"/> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jul 15 19:00:59 2025 +0000 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc"/> + </table> +</tables>
