Mercurial > repos > richard-burhans > segalign
changeset 14:f9e91add973c draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit eb6ee047d39760f2596b6e343e2dc3898fafc5cd
| author | richard-burhans |
|---|---|
| date | Mon, 29 Jul 2024 20:53:43 +0000 |
| parents | ae2cd39594eb |
| children | 99ee8d6f6815 |
| files | gapped_extension_options.xml output_options.xml segalign.xml segalign_output_options.xml test-data/segalign-output.maf.gz test-data/segalign-repeat-masker-output.tab.gz |
| diffstat | 6 files changed, 165 insertions(+), 273 deletions(-) [+] |
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--- a/gapped_extension_options.xml Sat Jul 13 16:51:52 2024 +0000 +++ b/gapped_extension_options.xml Mon Jul 29 20:53:43 2024 +0000 @@ -1,7 +1,6 @@ <macros> <xml name="gapped_extension_options"> <section name="gapped_extension_options" expanded="false" title="Gapped Extension Options"> - <param argument="--nogapped" type="boolean" checked="false" label="Don't perform gapped extension stage"/> <param argument="--ydrop" type="integer" value="9430" label="Y-drop value for gapped extension"/> <param argument="--gappedthresh" type="integer" value="" optional="true" label="Score threshold for gapped alignments"/> <param argument="--notrivial" type="boolean" checked="false" label="Don't output a trivial self-alignment block if the target and query sequences are identical"/>
--- a/output_options.xml Sat Jul 13 16:51:52 2024 +0000 +++ b/output_options.xml Mon Jul 29 20:53:43 2024 +0000 @@ -1,8 +1,95 @@ <macros> <xml name="output_options"> <section name="output_options" expanded="false" title="Output Options"> - <yield/> - <param argument="--markend" type="boolean" value="false" label="Write a marker line just before completion"/> + <conditional name="format"> + <param name="format_selector" type="select" display="radio" label="Specify the output format"> + <option value="bam">BAM --format=sam)</option> + <option value="general_def">General default (--format=general)</option> + <option value="general_full">Customized general (--format=general[:fields])</option> + <option value="maf" selected="true">MAF (--format=maf)</option> + <option value="blastn">blastn (--format=BLASTN)</option> + <option value="differences">Differences (--format=differences)</option> + </param> + <when value="bam"> + <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package"> + <option value="sam">BAM</option> + <option value="softsam">soft-clipped BAM</option> + <option value="sam-">BAM without header</option> + <option value="softsam-">soft-clipped BAM without header</option> + </param> + </when> + <when value="general_def"> + <!-- Do nothing --> + </when> + <when value="general_full"> + <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]"> + <option value="score" selected="true">score: Score of the alignment block</option> + <option value="name1" selected="true">name1: Name of the target sequence</option> + <option value="number1">number1: Number of the target sequence within the target file</option> + <option value="strand1" selected="true">strand1: Target sequence strand </option> + <option value="size1" selected="true">size1: Size of the entire target sequence</option> + <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option> + <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option> + <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option> + <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option> + <option value="text1">text1: Aligned characters in the target, including gap characters</option> + <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option> + <option value="nucs1">nucs1: The entire target sequence</option> + <option value="name2" selected="true">name2: Name of the query sequence</option> + <option value="number2">number2: Number of the query sequence within the query file</option> + <option value="strand2" selected="true">strand2: Query sequence strand</option> + <option value="size2" selected="true">size2: Size of the entire query sequence</option> + <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option> + <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option> + <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option> + <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option> + <option value="text2">text2: Aligned characters in the query, including gap characters</option> + <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option> + <option value="nucs2">nucs2: The entire query sequence</option> + <option value="nmatch">nmatch: Match count</option> + <option value="nmismatch">nmismatch: Mismatch count</option> + <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option> + <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option> + <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option> + <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option> + <option value="diff">diff: Differences between what would be written for text1 and text2</option> + <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option> + <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option> + <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option> + <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option> + <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option> + <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option> + <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option> + <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option> + <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option> + <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option> + <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option> + <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option> + <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option> + <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option> + <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option> + <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="%"/> + </valid> + </sanitizer> + </param> + </when> + <when value="maf"> + <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Select MAF flavor" help="MAF is a multiple alignment format developed at UCSC"> + <option value="maf">MAF</option> + <option value="maf+">MAF with additional stats</option> + <option value="maf-" selected="true">MAF without header and comments</option> + </param> + </when> + <when value="blastn"> + <!-- Do nothing --> + </when> + <when value="differences"> + <!-- Do nothing --> + </when> + </conditional> </section> </xml> </macros>
--- a/segalign.xml Sat Jul 13 16:51:52 2024 +0000 +++ b/segalign.xml Mon Jul 29 20:53:43 2024 +0000 @@ -8,7 +8,6 @@ <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"/> @@ -20,235 +19,135 @@ <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} +## Convert input to 2bit for lastz ------------------------------------- -## Mode ---------------------------------------------------------------- +mkdir -p "\$(pwd)/work" && +faToTwoBit <(gzip -cdfq '$target') "\$(pwd)/work/ref.2bit" && +faToTwoBit <(gzip -cdfq '$query') "\$(pwd)/work/query.2bit" && -#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 +## 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_output' + --diagonal-partition + --num-cpu \${GALAXY_SLOTS:-2} + --tool_directory '$__tool_directory__' + '$target' + '$query' ## Sequence Options ---------------------------------------------------- - --strand '$mode.sequence_options.strand_selector' -#if $segalign_mode == "segalign_repeat_masker" - --neighbor_proportion '$mode.sequence_options.neighbor_proportion' -#end if + --strand '$sequence_options.strand_selector' ## Scoring Options ----------------------------------------------------- -#set $scoring_pathname = str($mode.scoring_options.scoring) +#set $scoring_pathname = str($scoring_options.scoring) #if $scoring_pathname != "None": - --scoring '$scoring_pathname' + --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' +#if str($scoring_options.ambiguous_selector) != "x" + #if str($scoring_options.set_ambiguous_params_selector) == "true" + #set $argument_value = ','.join($scoring_options.ambiguous_selector, $scoring_options.ambiguous_reward, $scoring_options.ambiguous_penalty) + --ambiguous '$argument_value' #else - --ambiguous '$ambiguous_selector' + --ambiguous '$ambiguous_selector' #end if #end if ## Seeding Options ----------------------------------------------------- -#if str($mode.seeding_options.seed.seed_selector) == "custom" - --seed '$mode.seeding_options.seed.custom_seed' +#if str($seeding_options.seed.seed_selector) == "custom" + --seed '$seeding_options.seed.custom_seed' #else - --seed '$mode.seeding_options.seed.seed_selector' + --seed '$seeding_options.seed.seed_selector' #end if - --step '$mode.seeding_options.step' -#if str($mode.seeding_options.notransition) == "true" - --notransition + --step '$seeding_options.step' +#if str($seeding_options.notransition) == "true" + --notransition #end if ## Ungapped Extension Options ------------------------------------------ - --xdrop '$mode.ungapped_extension_options.xdrop' - --hspthresh '$mode.ungapped_extension_options.hspthresh' -#if str($mode.ungapped_extension_options.noentropy) == "true" - --noentropy + --xdrop '$ungapped_extension_options.xdrop' + --hspthresh '$ungapped_extension_options.hspthresh' +#if str($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 + --nogapped + --ydrop '$gapped_extension_options.ydrop' +#if str($gapped_extension_options.gappedthresh) != "" + --gappedthresh '$gapped_extension_options.gappedthresh' +#end if +#if str($gapped_extension_options.notrivial) == "true" + --notrivial #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 +#if str($output_options.format.format_selector) == "bam" + --format '$output_options.format.bam_options' +#else if str($output_options.format.format_selector) == "general_def" + --format general- +#else if str($output_options.format.format_selector) == "maf" + --format '$output_options.format.maf_type' +#else if str($output_options.format.format_selector) == "blastn" + --format=BLASTN- +#else if str($output_options.format.format_selector) == "general_full" + --format 'general-:${output_options.format.fields}' +#else if str($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": + ## #if str( $output_format.out.format ) == "bam": ## | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}' - ## .else: + ## #else: ## > '${output}' - ## .end if - ## .if $output_format.rplot: + ## #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 + ## #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($mode.system_options.debug) == "true" - --debug + --wga_chunk_size '$system_options.wga_chunk_size' + --lastz_interval_size '$system_options.lastz_interval_size' + --seq_block_size '$system_options.seq_block_size' + --num_gpu '$system_options.num_gpu' +#if str($system_options.debug) == "true" + --debug #end if -## ------------------------------------------------------------------- +## Package Output ---------------------------------------------------- -#if $segalign_mode == "segalign_diagonal_partition" - && - python '$__tool_directory__/package_output.py' - --tool_directory '$__tool_directory__' -#end if + && python '$__tool_directory__/package_output.py' ]]></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> + <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="system_options"/> </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> + <data name="segalign_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign on ${on_string}"/> </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"> + <output name="segalign_output" ftype="tgz"> <assert_contents> <has_archive_member path="galaxy/commands.json"/> </assert_contents>
--- a/segalign_output_options.xml Sat Jul 13 16:51:52 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -<macros> - <xml name="segalign_output_options"> - <conditional name="format"> - <param name="format_selector" type="select" display="radio" label="Specify the output format"> - <option value="bam">BAM --format=sam)</option> - <option value="general_def">General default (--format=general)</option> - <option value="general_full">Customized general (--format=general[:fields])</option> - <option value="maf" selected="true">MAF (--format=maf)</option> - <option value="blastn">blastn (--format=BLASTN)</option> - <option value="differences">Differences (--format=differences)</option> - </param> - <when value="bam"> - <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package"> - <option value="sam">BAM</option> - <option value="softsam">soft-clipped BAM</option> - <option value="sam-">BAM without header</option> - <option value="softsam-">soft-clipped BAM without header</option> - </param> - </when> - <when value="general_def"> - <!-- Do nothing --> - </when> - <when value="general_full"> - <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]"> - <option value="score" selected="true">score: Score of the alignment block</option> - <option value="name1" selected="true">name1: Name of the target sequence</option> - <option value="number1">number1: Number of the target sequence within the target file</option> - <option value="strand1" selected="true">strand1: Target sequence strand </option> - <option value="size1" selected="true">size1: Size of the entire target sequence</option> - <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option> - <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option> - <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option> - <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option> - <option value="text1">text1: Aligned characters in the target, including gap characters</option> - <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option> - <option value="nucs1">nucs1: The entire target sequence</option> - <option value="name2" selected="true">name2: Name of the query sequence</option> - <option value="number2">number2: Number of the query sequence within the query file</option> - <option value="strand2" selected="true">strand2: Query sequence strand</option> - <option value="size2" selected="true">size2: Size of the entire query sequence</option> - <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option> - <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option> - <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option> - <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option> - <option value="text2">text2: Aligned characters in the query, including gap characters</option> - <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option> - <option value="nucs2">nucs2: The entire query sequence</option> - <option value="nmatch">nmatch: Match count</option> - <option value="nmismatch">nmismatch: Mismatch count</option> - <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option> - <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option> - <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option> - <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option> - <option value="diff">diff: Differences between what would be written for text1 and text2</option> - <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option> - <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option> - <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option> - <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option> - <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option> - <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option> - <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option> - <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option> - <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option> - <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option> - <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option> - <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option> - <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option> - <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option> - <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option> - <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="%"/> - </valid> - </sanitizer> - </param> - </when> - <when value="maf"> - <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Select MAF flavor" help="MAF is a multiple alignment format developed at UCSC"> - <option value="maf">MAF</option> - <option value="maf+">MAF with additional stats</option> - <option value="maf-" selected="true">MAF without header and comments</option> - </param> - </when> - <when value="blastn"> - <!-- Do nothing --> - </when> - <when value="differences"> - <!-- Do nothing --> - </when> - </conditional> - </xml> -</macros>