mumemto: auto-generated tool wrapper (issue #1929) #1931
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| description: Mumemto - efficient maximal matching across pangenomes | ||
| categories: | ||
| - Sequence Analysis | ||
| owner: bgruening | ||
| homepage_url: https://github.com/vikshiv/mumemto | ||
| long_description: | | ||
| Mumemto is a tool for finding maximal unique matches (multi-MUMs) and | ||
| maximal exact matches (multi-MEMs) across pangenomes using prefix-free | ||
| parsing (PFP). It includes subcommands for visualization, coverage | ||
| analysis, collinear block detection, format conversion, sequence | ||
| extraction, BED conversion, partition merging, and inversion detection. | ||
| remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/mumemto | ||
| type: unrestricted | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Wrapper for mumemto application {{ tool_name }}." | ||
| suite: | ||
| name: "suite_mumemto" | ||
| description: "A suite of Galaxy tools for the mumemto pangenome matching toolkit" | ||
| type: repository_suite_definition |
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| <macros> | ||
| <token name="@TOOL_VERSION@">1.4.1</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">25.0</token> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">mumemto</requirement> | ||
| </requirements> | ||
| </xml> | ||
| <xml name="version_command"> | ||
| <!-- this can be replaces by mumento --version 2>&1 once version 1.4.2 is released --> | ||
| <version_command><![CDATA[echo "mumemto @TOOL_VERSION@"]]></version_command> | ||
| </xml> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1186/s13059-025-03644-0</citation> | ||
| </citations> | ||
| </xml> | ||
| <!-- Reusable MUMs file input --> | ||
| <xml name="input_mums"> | ||
| <param argument="-m" type="data" format="txt" label="MUMs file" help="Output .mums file from mumemto. Binary .bumbl files must be converted with mumemto convert first"/> | ||
| </xml> | ||
| <!-- Reusable lengths file input --> | ||
| <xml name="input_lengths"> | ||
| <param argument="-l" type="data" format="txt" label="Lengths file" help="Output .lengths file from mumemto"/> | ||
|
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| </xml> | ||
| <!-- Shared configfile for the -f (filelist) flag. The param itself is inlined | ||
| in each tool because -f does different things: viz reorders sequences, | ||
| inversion relabels them 1:1 by position. --> | ||
| <xml name="configfile_filelist"> | ||
| <configfiles> | ||
| <configfile name="filelist_file">$filelist_text</configfile> | ||
| </configfiles> | ||
| </xml> | ||
| <!-- Reusable length filter param --> | ||
| <xml name="param_length_filter"> | ||
| <param argument="-L" type="integer" value="0" min="0" label="Length filter" help="Only consider MUMs of at least this length"/> | ||
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| </xml> | ||
| <!-- Reusable max gap param --> | ||
| <xml name="param_max_gap"> | ||
| <param argument="-g" type="integer" value="1000" min="0" label="Maximum gap length" help="Maximum allowed gap between collinear MUMs"/> | ||
| </xml> | ||
| <!-- Contig spacer, shared by the multi-FASTA layout modes of mumemto viz --> | ||
| <xml name="param_spacer"> | ||
| <param argument="--spacer" type="float" value="0.1" min="0" max="1" label="Contig spacer" help="Gap drawn between contigs, as a fraction of the longest contig's length"/> | ||
| </xml> | ||
| </macros> | ||
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| <tool id="mumemto" name="mumemto" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>compute multi-MUMs and multi-MEMs across pangenomes</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <expand macro="version_command"/> | ||
| <command detect_errors="aggressive"><![CDATA[ | ||
| #import re | ||
| ## The file list is built here rather than taken from the user: mumemto resolves the | ||
| ## paths inside it, and any path a user could supply would point outside the job. | ||
| ## names.tsv maps the path mumemto will record to the dataset name, see the awk below. | ||
| #for $i, $fasta in enumerate($input_fasta): | ||
| ln -s '$fasta' 'seq_${i}.fa' && | ||
| echo 'seq_${i}.fa' >> filelist.txt && | ||
| printf '%s\t%s\n' "\$(readlink -f 'seq_${i}.fa')" '${re.sub("[^\w.-]", "_", str($fasta.element_identifier))}' >> names.tsv && | ||
| #end for | ||
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| mumemto | ||
| -i filelist.txt | ||
| -o 'output' | ||
| -l $l | ||
| #if str($k): | ||
| -k $k | ||
| #end if | ||
| #if str($F): | ||
| -F $F | ||
| #end if | ||
| $no_revcomp | ||
| #if str($matches.match_type) == "mum": | ||
| ## -f 1 is what makes a match unique, i.e. a MUM rather than a MEM | ||
| -f 1 | ||
| $matches.b | ||
| #if str($matches.merge.mode) != "none": | ||
| -M | ||
| #if str($matches.merge.mode) == "anchor": | ||
| -n | ||
| #end if | ||
| #end if | ||
| #else: | ||
| -f $matches.f | ||
| #end if | ||
| -w $advanced.w | ||
| -m $advanced.m | ||
| $advanced.g | ||
| $advanced.K | ||
| && | ||
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| ## mumemto records each input's canonicalised path in the .lengths file, which resolves | ||
| ## the symlinks above to opaque Galaxy dataset paths. Substitute the dataset names back: | ||
| ## the rest of the suite reads this column for sequence labels, and mumemto merge matches | ||
| ## partitions by the basename on its first line. | ||
| awk 'NR == FNR { name[\$1] = \$2; next } \$1 in name { \$1 = name[\$1] } { print }' names.tsv output.lengths > relabelled.lengths && | ||
| mv relabelled.lengths output.lengths | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_fasta" type="data" format="fasta,fasta.gz" multiple="true" min="2" label="Input FASTA files" help="Two or more genome sequences, one dataset per genome or haplotype. Their order here becomes the column order in the output."/> | ||
| <param argument="-l" type="integer" value="20" min="1" label="Minimum match length" help="Minimum length of a match to report"/> | ||
| <param argument="-k" type="integer" optional="true" label="Minimum genomes" help="Minimum number of sequences a match must appear in. Negative values are relative to the number of sequences, so -1 means all but one. Leave empty to require every sequence."/> | ||
| <param argument="-F" type="integer" optional="true" label="Maximum total frequency" help="Maximum total occurrences across all sequences. Negative values are relative to the number of sequences. Leave empty for no limit."/> | ||
| <param argument="--no-revcomp" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Exclude reverse complement matches" help="By default matches on the reverse strand are included"/> | ||
| <conditional name="matches"> | ||
| <param name="match_type" type="select" label="Match type" help="Unique matches are the usual starting point for pangenome analysis; the rest of the suite is built around them."> | ||
| <option value="mum" selected="true">Multi-MUMs - each match occurs at most once per sequence</option> | ||
| <option value="mem">Multi-MEMs - a match may repeat within a sequence</option> | ||
| </param> | ||
| <when value="mum"> | ||
| <param argument="-b" type="boolean" truevalue="-b" falsevalue="" checked="false" label="Write the binary BUMbl format instead of text" help="Replaces the text .mums output with a compact binary .bumbl file that downstream tools load faster. You do not get both."/> | ||
| <conditional name="merge"> | ||
| <param name="mode" type="select" label="Also write metadata for merging partitions" help="Needed only if this run is one partition of a larger collection that will later be combined with the mumemto merge tool."> | ||
| <option value="none" selected="true">No</option> | ||
| <option value="anchor">Yes, for anchor-based merging</option> | ||
| <option value="string">Yes, for string-based merging</option> | ||
| </param> | ||
| <when value="none"/> | ||
| <when value="anchor"/> | ||
| <when value="string"/> | ||
| </conditional> | ||
| </when> | ||
| <when value="mem"> | ||
| <param argument="-f" type="integer" value="0" min="0" label="Maximum occurrences per sequence" help="0 for no limit. Any value other than 1 produces multi-MEMs; a value of 1 is rejected here because it makes mumemto write a .mums file instead, which is the Multi-MUMs match type above."> | ||
| <validator type="expression" message="A value of 1 produces MUMs, not MEMs. Switch match type to Multi-MUMs instead.">value != 1</validator> | ||
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| </param> | ||
| </when> | ||
| </conditional> | ||
| <section name="advanced" title="Advanced options" expanded="false"> | ||
| <param argument="-w" type="integer" value="10" min="1" label="PFP window size" help="Prefix-free parsing window size."/> | ||
| <param argument="-m" type="integer" value="100" min="1" label="PFP hash modulus" help="Prefix-free parsing hash modulus."/> | ||
| <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Use gsacak directly" help="Use gsacak instead of the built-in suffix array construction."/> | ||
| <param argument="-K" type="boolean" truevalue="-K" falsevalue="" label="Keep temporary files" help="Retain PFP intermediate files for debugging."/> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="lengths_output" format="txt" from_work_dir="output.lengths" label="${tool.name} lengths on ${on_string}"/> | ||
| <!-- mumemto writes .mums only for unique matches, and swaps it for .bumbl when the | ||
| binary format is requested, so this is not an unconditional output. --> | ||
| <data name="mums_output" format="txt" from_work_dir="output.mums" label="${tool.name} MUMs on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mum' and not matches['b']</filter> | ||
| </data> | ||
| <data name="bumbl_output" format="binary" from_work_dir="output.bumbl" label="${tool.name} BUMbl on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mum' and matches['b']</filter> | ||
| </data> | ||
| <!-- Any -f other than 1 makes mumemto write .mems instead, with an extra column --> | ||
| <data name="mems_output" format="txt" from_work_dir="output.mems" label="${tool.name} MEMs on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mem'</filter> | ||
| </data> | ||
| <data name="thresh_output" format="binary" from_work_dir="output.thresh" label="${tool.name} thresholds on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mum' and matches['merge']['mode'] == 'string'</filter> | ||
| </data> | ||
| <data name="thresh_rev_output" format="binary" from_work_dir="output.thresh_rev" label="${tool.name} reverse thresholds on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mum' and matches['merge']['mode'] == 'string'</filter> | ||
| </data> | ||
| <!-- Anchor mode replaces the two .thresh files with a single .athresh --> | ||
| <data name="athresh_output" format="binary" from_work_dir="output.athresh" label="${tool.name} anchor thresholds on ${on_string}"> | ||
| <filter>matches['match_type'] == 'mum' and matches['merge']['mode'] == 'anchor'</filter> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <!-- Strict multi-MUMs: seq1 and seq2 share one 200 bp block --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_fasta" value="seq1.fa,seq2.fa" ftype="fasta"/> | ||
| <param name="l" value="10"/> | ||
| <output name="mums_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="1"/> | ||
| <has_line line="200	40,50	+,+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <!-- The record names and totals come from the FASTA itself, so they are stable. | ||
| No "/" anywhere proves the dataset paths mumemto writes were relabelled. --> | ||
| <output name="lengths_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
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| <has_line_matching expression="^\S+ \* 240$"/> | ||
| <has_line_matching expression="^\S+ seq1 240$"/> | ||
| <has_line_matching expression="^\S+ seq2 299$"/> | ||
| <not_has_text text="/"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- Multi-MEMs: a fourth column of sequence indices appears, and the reverse | ||
| strand copy of the same block shows up as a second match --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_fasta" value="seq1.fa,seq2.fa" ftype="fasta"/> | ||
| <param name="l" value="200"/> | ||
| <conditional name="matches"> | ||
| <param name="match_type" value="mem"/> | ||
| <param name="f" value="0"/> | ||
| </conditional> | ||
| <output name="mems_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="2"/> | ||
| <has_line line="200	40,50	0,1	+,+"/> | ||
| <has_line line="200	50,41	1,0	-,-"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="lengths_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- Binary output replaces the text MUMs file, so only two outputs appear --> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_fasta" value="seq1.fa,seq2.fa" ftype="fasta"/> | ||
| <param name="l" value="10"/> | ||
| <conditional name="matches"> | ||
| <param name="match_type" value="mum"/> | ||
| <param name="b" value="true"/> | ||
| </conditional> | ||
| <output name="bumbl_output" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="39"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="lengths_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- String-based merge metadata: two threshold files alongside the MUMs --> | ||
| <test expect_num_outputs="4"> | ||
| <param name="input_fasta" value="seq1.fa,seq2.fa" ftype="fasta"/> | ||
| <param name="l" value="10"/> | ||
| <conditional name="matches"> | ||
| <param name="match_type" value="mum"/> | ||
| <conditional name="merge"> | ||
| <param name="mode" value="string"/> | ||
| </conditional> | ||
| </conditional> | ||
| <output name="mums_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="1"/> | ||
| <has_line line="200	40,50	+,+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="lengths_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="thresh_output" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="402"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="thresh_rev_output" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="402"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- Anchor-based merge metadata: a single .athresh instead of the two above, | ||
| which is what the mumemto merge tool consumes --> | ||
| <test expect_num_outputs="3"> | ||
| <param name="input_fasta" value="seq1.fa,seq2.fa" ftype="fasta"/> | ||
| <param name="l" value="10"/> | ||
| <conditional name="matches"> | ||
| <param name="match_type" value="mum"/> | ||
| <conditional name="merge"> | ||
| <param name="mode" value="anchor"/> | ||
| </conditional> | ||
| </conditional> | ||
| <output name="mums_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="1"/> | ||
| <has_line line="200	40,50	+,+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="lengths_output" ftype="txt"> | ||
| <assert_contents> | ||
| <has_n_lines n="4"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="athresh_output" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="482"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help format="markdown"><![CDATA[ | ||
| **What it does** | ||
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| Mumemto finds maximal unique matches (multi-MUMs) and maximal exact matches | ||
| (multi-MEMs) across a collection of genome sequences (a pangenome). A MUM is a | ||
| substring that appears exactly once in every input sequence; a MEM relaxes that | ||
| to allow repeats within a sequence. Mumemto uses prefix-free parsing (PFP) for | ||
| efficient computation on large genomes. | ||
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| By default it computes strict multi-MUMs: matches that appear exactly once in | ||
| every input sequence. Two settings relax that requirement: | ||
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| - **Minimum genomes:** accept matches present in only some of the sequences. | ||
| Negative values count back from the total, so -1 means all but one. | ||
| - **Match type:** switching to multi-MEMs lets a match repeat within a sequence. | ||
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| ----- | ||
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| **Input** | ||
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| Two or more FASTA datasets, one per genome or haplotype. The order you select | ||
| them in is the order of the coordinate columns in the output, and the first one | ||
| becomes the anchor for anchor-based merging. | ||
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| ----- | ||
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| **Output** | ||
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| Always a `.lengths` file recording each input file and the length of every record | ||
| in it. Downstream tools in this suite need it alongside the matches. | ||
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| Then, depending on the settings, exactly one file of matches: | ||
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| - **`.mums`** — tab separated: match length, then one start position per sequence, | ||
| then one strand per sequence | ||
| - **`.bumbl`** — the same information packed into binary, chosen instead of `.mums` | ||
| rather than in addition to it | ||
| - **`.mems`** — written when the match type is multi-MEMs. It carries an extra | ||
| column between the positions and the strands giving the sequence each position | ||
| belongs to, because a match may occur several times in one sequence. | ||
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| Requesting merge metadata adds either `.thresh` and `.thresh_rev` (string-based) | ||
| or a single `.athresh` (anchor-based). Only anchor-based output can be combined | ||
| by the *mumemto merge* tool. | ||
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| ----- | ||
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| **Downstream tools** | ||
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| The rest of the suite consumes the `.mums` and `.lengths` pair: synteny plots, | ||
| coverage, collinear blocks, inversions, BED conversion, MUM sequence extraction, | ||
| format conversion and partition merging. | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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Not sure users know what those mms and bumbl files are.
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These are the output files generated by
mumento_convert. We can more info in the help desc