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Richard C. Burhans committed Apr 16, 2024
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<tool id="segalign" name="SegAlign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm</description>
<macros>
<import>macros.xml</import>
<import>sequence_options.xml</import>
<import>scoring_options.xml</import>
<import>seeding_options.xml</import>
<import>ungapped_extension_options.xml</import>
<import>gapped_extension_options.xml</import>
<import>output_options.xml</import>
<import>segalign_output_options.xml</import>
<import>system_options.xml</import>
</macros>
<expand macro="edam_ontology"/>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
##
## https://www.gnu.org/software/coreutils/manual/html_node/nproc-invocation.html
##
## If the OMP_NUM_THREADS or OMP_THREAD_LIMIT environment variables
## are set, then they will determine the minimum and maximum returned
## value respectively.
##
## This is how you tame nproc(1)
##
OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
## Mode ----------------------------------------------------------------
#if str($mode.mode_selector) == "segalign"
#if str($mode.diagonal_partition_options.diagonal_partition) == "true"
#set $segalign_mode = "segalign_diagonal_partition"
'$__tool_directory__/run_segalign_diagonal_partition'
--tool_directory '$__tool_directory__'
--max_segments '$mode.diagonal_partition_options.max_segments'
#else
#set $segalign_mode = "segalign"
run_segalign
#end if
'$mode.target'
'$mode.query'
#else if str($mode.mode_selector) == "segalign_repeat_masker"
#set $segalign_mode = "segalign_repeat_masker"
run_segalign_repeat_masker
'$mode.seq_file'
#end if
## Sequence Options ----------------------------------------------------
--strand '$mode.sequence_options.strand_selector'
#if $segalign_mode == "segalign_repeat_masker"
--neighbor_proportion '$mode.sequence_options.neighbor_proportion'
#end if
## Scoring Options -----------------------------------------------------
#set $scoring_pathname = str($mode.scoring_options.scoring)
#if $scoring_pathname != "None":
--scoring '$scoring_pathname'
#end if
## Seeding Options -----------------------------------------------------
#if str($mode.seeding_options.seed.seed_selector) == "custom"
--seed '$mode.seeding_options.seed.custom_seed'
#else
--seed '$mode.seeding_options.seed.seed_selector'
#end if
--step '$mode.seeding_options.step'
#if str($mode.seeding_options.notransition) == 'true'
--notransition
#end if
## Ungapped Extension Options ------------------------------------------
--xdrop '$mode.ungapped_extension_options.xdrop'
--hspthresh '$mode.ungapped_extension_options.hspthresh'
#if str($mode.ungapped_extension_options.noentropy) == 'true'
--noentropy
#end if
## Gapped Extension Options --------------------------------------------
#if $segalign_mode != "segalign_repeat_masker"
#if str($mode.gapped_extension_options.nogapped) == 'true'
--nogapped
#end if
--ydrop '$mode.gapped_extension_options.ydrop'
#if str($mode.gapped_extension_options.gappedthresh) != ""
--gappedthresh '$mode.gapped_extension_options.gappedthresh'
#end if
#if str($mode.gapped_extension_options.notrivial) == 'true'
--notrivial
#end if
#end if
## Output Options -----------------------------------------------------
#if $segalign_mode != "segalign_repeat_masker"
#if str($mode.output_options.format.format_selector) == "bam"
--format '$mode.output_options.format.bam_options'
#else if str($mode.output_options.format.format_selector) == "general_def"
--format general-
#else if str($mode.output_options.format.format_selector) == "general_full"
--format 'general-:${mode.output_options.format.fields}'
#else if str($mode.output_options.format.format_selector) == "maf"
--format '$mode.output_options.format.maf_type'
#else if str($mode.output_options.format.format_selector) == "blastn"
--format=BLASTN-
#else if str($mode.output_options.format.format_selector) == "differences"
--format=differences
#end if
## TODO :: rplot, bam
## --action:target=multiple
## $output_format.rplot
## .if str( $output_format.out.format ) == "bam":
## | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
## .else:
## > '${output}'
## .end if
## .if $output_format.rplot:
## &&
## Rscript $r_plot > /dev/null 2>&1
## .end if
#if $segalign_mode == "segalign"
--output '$segalign_output'
#end if
#else if $segalign_mode == "segalign_repeat_masker"
--M '$mode.output_options.M'
--output '$segalign_repeat_masker_output'
#end if
#if str($mode.output_options.markend) == 'true'
--markend
#end if
## System Options -----------------------------------------------------
--wga_chunk_size '$mode.system_options.wga_chunk_size'
--lastz_interval_size '$mode.system_options.lastz_interval_size'
--seq_block_size '$mode.system_options.seq_block_size'
--num_gpu '$mode.system_options.num_gpu'
#if str($mode.system_options.debug) == 'true'
--debug
#end if
#if $segalign_mode == "segalign_diagonal_partition"
&&
'$__tool_directory__/package_output.py'
#end if
## -------------------------------------------------------------------
]]></command>
<inputs>
<conditional name="mode">
<param name="mode_selector" type="select" label="Choose the mode">
<option value="segalign" selected="true">SegAlign</option>
<option value="segalign_repeat_masker">SegAlign repeat masker</option>
</param>
<when value="segalign">
<param name="target" type="data" format="fasta" label="Target sequence file in FASTA format" />
<param name="query" type="data" format="fasta" label="Query sequence file in FASTA format" />
<expand macro="sequence_options" />
<expand macro="scoring_options"/>
<expand macro="seeding_options" />
<expand macro="ungapped_extension_options"/>
<expand macro="gapped_extension_options"/>
<expand macro="output_options">
<expand macro="segalign_output_options"/>
</expand>
<expand macro="system_options" />
<section name="diagonal_partition_options" title="Diagonal Partition Options">
<param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization" />
<param argument="--max_segments" type="integer" value="20000" label="Max segments" />
</section>
</when>
<when value="segalign_repeat_masker">
<param name="seq_file" type="data" format="fasta" label="Sequence file in FASTA format" />
<expand macro="sequence_options">
<param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to" />
</expand>
<expand macro="scoring_options"/>
<expand macro="seeding_options" />
<expand macro="ungapped_extension_options"/>
<expand macro="output_options">
<param argument="--M" type="integer" value="1" max="255" label="report any position that is covered by at least this many alignments; the maximum allowed depth is 255" />
</expand>
<expand macro="system_options" />
</when>
</conditional>
</inputs>
<outputs>
<data name="segalign_output" format="tabular" label="SegAlign on ${on_string}">
<change_format>
<when input="mode.output_options.format.format_selector" value="bam" format="bam" />
<when input="mode.output_options.format.format_selector" value="maf" format="maf" />
<when input="mode.output_options.format.format_selector" value="differences" format="interval" />
</change_format>
<filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is False</filter>
</data>
<data name="segalign_diagonal_partition_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign Diagonal Partition on ${on_string}">
<filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is True</filter>
</data>
<data name="segalign_repeat_masker_output" format="tabular" label="SegAlign Repeat Masker on ${on_string}">
<filter>mode['mode_selector'] == 'segalign_repeat_masker'</filter>
</data>
</outputs>
<tests>
<test>
<param name="target" value="hg38.chr20.chunk.fa.gz" type="fasta" />
<param name="query" value="mm39.chr2.chunk.fa.gz" type="fasta" />
<output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf" />
</test>
</tests>
<help><![CDATA[
SegAlign is a scalable, GPU-accelerated system for computing pairwise WGA. SegAlign is based on the standard seed-filter-extend heuristic, in which the filtering stage dominates the runtime (e.g. 98% for human-mouse WGA), and is accelerated using GPU(s).
https://github.com/gsneha26
]]></help>
<expand macro="citations"/>
</tool>

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