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view segalign.xml @ 10:ec709ce3d91b draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 701d5b6d0b25dbd9d2a8c08234f3aca7ef502131
author | richard-burhans |
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date | Thu, 11 Jul 2024 15:50:48 +0000 |
parents | 08e987868f0f |
children | 168b0a92edd3 |
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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"/> <required_files> <include path="diagonal_partition.py"/> <include path="lastz-cmd.ini"/> <include path="package_output.py"/> <include path="runner.py"/> </required_files> <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.gapped_extension_options.nogapped) == "false" mkdir -p "\$(pwd)/work" && faToTwoBit <(gzip -cdfq '$mode.target') "\$(pwd)/work/ref.2bit" && faToTwoBit <(gzip -cdfq '$mode.query') "\$(pwd)/work/query.2bit" && #end if #if str($mode.diagonal_partition_options.diagonal_partition) == "true" #set $segalign_mode = "segalign_diagonal_partition" ## explicitly calling python to bypass a pulsar bug ## https://github.com/galaxyproject/pulsar/issues/341 python '$__tool_directory__/runner.py' --output-type tarball --output-file '$segalign_diagonal_partition_output' --diagonal-partition --num-cpu \${GALAXY_SLOTS:-2} --tool_directory '$__tool_directory__' #else #set $segalign_mode = "segalign" python '$__tool_directory__/runner.py' --output-type output --output-file '$segalign_output' --num-cpu \${GALAXY_SLOTS:-2} --tool_directory '$__tool_directory__' #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' --num_cpu \${GALAXY_SLOTS:-2} #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 #if str($mode.scoring_options.ambiguous_selector) != "x" #if str($mode.scoring_options.set_ambiguous_params_selector) == "true" #set $argument_value = ','.join($mode.scoring_options.ambiguous_selector, $mode.scoring_options.ambiguous_reward, $mode.scoring_options.ambiguous_penalty) --ambiguous '$argument_value' #else --ambiguous '$ambiguous_selector' #end if #end if ## Seeding Options ----------------------------------------------------- #if str($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 #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 $segalign_mode == "segalign_diagonal_partition" && python '$__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,fasta.gz" label="Target sequence file in FASTA format"/> <param name="query" type="data" format="fasta,fasta.gz" 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" expanded="false" title="Diagonal Partition Options"> <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/> </section> </when> <when value="segalign_repeat_masker"> <param name="seq_file" type="data" format="fasta,fasta.gz" 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 expect_num_outputs="1" expect_test_failure="true"> <param name="mode_selector" value="segalign"/> <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/> </test> <test expect_num_outputs="1" expect_test_failure="true"> <param name="mode_selector" value="segalign_repeat_masker"/> <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/> </test> <test expect_num_outputs="1" expect_test_failure="true"> <param name="mode_selector" value="segalign"/> <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> <param name="diagonal_partition" value="true"/> <output name="segalign_diagonal_partition_output" ftype="tgz"> <assert_contents> <has_archive_member path="galaxy/commands.json"/> </assert_contents> </output> </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>