Mercurial > repos > p.lucas > diamond_using_binary
changeset 64:4c0effbfd084 draft
Uploaded
| author | p.lucas |
|---|---|
| date | Mon, 10 Jun 2024 13:17:15 +0000 |
| parents | f35c3ad107ab |
| children | 45f0db6a8025 |
| files | diamond.xml |
| diffstat | 1 files changed, 376 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diamond.xml Mon Jun 10 13:17:15 2024 +0000 @@ -0,0 +1,376 @@ +<tool id="pl_diamond" name="PL_Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01"> + <description>alignment tool for short sequences against a protein database</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"> +<![CDATA[ + + #if $ref_db_source.db_source == "history": + ln -s $ref_db_source.reference_database ./database.dmnd< + #end if + + && + + /usr/bin/diamond + $method_cond.method_select + --quiet + --threads "\${GALAXY_SLOTS:-12}" + #if $ref_db_source.db_source == "history": + --db ./database + #else + --db $ref_db_source.index.fields.db_path + #end if + --query '$query' + #if $method_cond.method_select == "blastx" + --query-gencode '$method_cond.query_gencode' + --strand '$method_cond.query_strand' + --min-orf $method_cond.min_orf + #if $method_cond.frameshift_cond.frameshift_select == 'yes' + --frameshift $method_cond.frameshift_cond.frameshift + $method_cond.frameshift_cond.range_culling + #end if + #else if $method_cond.method_select == "blastp" + $method_cond.no_self_hits + #end if + + @OUTPUT_ARGS@ + + #if $output_section.output.outfmt != '100' + --compress '0' + #end if + $sens_cond.sensitivity + $iterate + --algo $algo + #if $global_ranking + --global-ranking $global_ranking + #end if + #if str($gapopen) != "": + --gapopen '$gapopen' + #end if + #if str($gapextend) != "": + --gapextend '$gapextend' + #end if + --matrix '$matrix' + --comp-based-stats '$method_cond.comp_based_stats' + --masking '$masking' + + @HITFILTER_ARGS@ + + #if str($filter_score.filter_score_select) == 'evalue': + --evalue '$filter_score.evalue' + #else: + --min-score '$filter_score.min_score' + #end if + + --id '$id' + --query-cover '$query_cover' + --subject-cover '$subject_cover' + --block-size '$sens_cond.block_size' + #if $output_section.output_unal + #if "--un" in $output_section.output_unal + --un '$unalqueries' + #if $query.ext.startswith("fasta"): + --unfmt fasta + #else + --unfmt fastq + #end if + #end if + #if "--al" in $output_section.output_unal + --al '$alqueries' + #if $query.ext.startswith("fasta"): + --alfmt fasta + #else + --alfmt fastq + #end if + #end if + #end if + #if $output_section.max_hsps + --max-hsps $output_section.max_hsps + #end if + #if $tax_cond.tax_select == 'file': + --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'` + #else if $tax_cond.tax_select == 'list': + --taxonlist '$tax_cond.taxonlist' + #end if + #if $advanced_section.seed_cut + --seed-cut $advanced_section.seed_cut + #end if + $advanced_section.freq_masking + --motif-masking $advanced_section.motif_masking +]]> + </command> + <inputs> + <conditional name="method_cond"> + <param name="method_select" type="select" label="Alignment mode" help="(blastp/blastx)"> + <option value="blastp">Amino acid query sequences (blastp)</option> + <option value="blastx">DNA query sequences (blastx)</option> + </param> + <when value="blastx"> + <param argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help=""> + <option value="1">Standard Code</option> + <option value="2">Vertebrate Mitochondrial Code</option> + <option value="3">Yeast Mitochondrial Code</option> + <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">Invertebrate Mitochondrial Code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">Echinoderm and Flatworm Mitochondrial Code</option> + <option value="10">Euplotid Nuclear Code</option> + <option value="11">Bacterial, Archaeal and Plant Plastid Code</option> + <option value="12">Alternative Yeast Nuclear Code</option> + <option value="13">Ascidian Mitochondrial Code</option> + <option value="14">Alternative Flatworm Mitochondrial Code</option> + <option value="16">Chlorophycean Mitochondrial Code</option> + <option value="21">Trematode Mitochondrial Code</option> + <option value="22">Scenedesmus obliquus Mitochondrial Code</option> + <option value="23">Thraustochytrium Mitochondrial Code</option> + <option value="24">Pterobranchia Mitochondrial Code</option> + <option value="25">Candidate Division SR1 and Gracilibacteria Code</option> + <option value="26">Pachysolen tannophilus Nuclear Code</option> + </param> + <param argument="--min-orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" /> + + <param name="query_strand" argument="--strand" type="select" label="query strands to search" help=""> + <option value="both" selected="True">Both</option> + <option value="plus">Plus</option> + <option value="minus">Minus</option> + </param> + <conditional name="frameshift_cond"> + <param name="frameshift_select" type="select" label="Allow for frameshifts?" help=""> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param argument="--range-culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/> + <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." /> + </when> + <when value="no"/> + </conditional> + + <param argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"> + <option value="0">Disable</option> + <option value="1" selected="True">Default mode (Hauser, 2016)</option> + </param> + </when> + <when value="blastp"> + <param argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true" + label="Suppress reporting of identical self-hits between sequences" + help="The FASTA sequence identifiers as well as the sequences of query and target need to be identical for a hit to be deleted"/> + + <param argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"> + <option value="0">Disable</option> + <option value="1" selected="True">Default mode (Hauser, 2016)</option> + <option value="2">Compositional matrix adjust conditioned on sequence properties, simplified (Yu, 2005)</option> + <option value="3">Compositional matrix adjust conditioned on sequence properties (Yu, 2005)</option> + <option value="4">Compositional matrix adjust unconditionally (Yu, 2005)</option> + </param> + </when> + </conditional> + <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> + <conditional name="ref_db_source"> + <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin"> + <options from_data_table="pl_diamond_database"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="reference_database" argument="--db" type="data" format="dmnd" label="Select the reference database" /> + </when> + </conditional> + <conditional name="tax_cond"> + <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against."> + <option value="no" selected="True">No</option> + <option value="list">List of taxids entered manually</option> + <option value="file">List of taxids from single column tabular file</option> + </param> + <when value="no"/> + <when value="list"> + <param name="taxonlist" argument="--taxonlist" type="text" value="" label="Comma separated list of taxon ids" help=""> + <validator type="regex" message="Taxonlist needs to be a comma separated list of integers">[0-9,]*</validator> + </param> + </when> + <when value="file"> + <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" /> + </when> + </conditional> + <conditional name="sens_cond"> + <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time."> + <option value="--fast">Fast (--fast)</option> + <option value="" selected="True">Default</option> + <option value="--mid-sensitive">Mid Sensitive (--mid-sensitive)</option> + <option value="--sensitive">Sensitive (--sensitive)</option> + <option value="--more-sensitive">More Sensitive (--more-sensitive)</option> + <option value="--very-sensitive">Very Sensitive (--very-sensitive)</option> + <option value="--ultra-sensitive">Ultra Sensitive (--ultra-sensitive)</option> + </param> + <when value="--fast"> + <expand macro="block_size_low_sens"/> + </when> + <when value=""> + <expand macro="block_size_low_sens"/> + </when> + <when value="--mid-sensitive"> + <expand macro="block_size_low_sens"/> + </when> + <when value="--sensitive"> + <expand macro="block_size_low_sens"/> + </when> + <when value="--more-sensitive"> + <expand macro="block_size_low_sens"/> + </when> + <when value="--very-sensitive"> + <expand macro="block_size_hi_sens"/> + </when> + <when value="--ultra-sensitive"> + <expand macro="block_size_hi_sens"/> + </when> + </conditional> + <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties"> + <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option> + <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option> + <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option> + <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option> + <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option> + <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option> + <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option> + <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option> + </param> + <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="Leave empty for default (see scoring matrix)" /> + <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="Leave empty for default (see scoring matrix)" /> + <param argument="--masking" type="select" label="Masking algorithm" help="DIAMOND by default applies the tantan repeat masking algorithm to the query and target sequences as described in (Frith, 2011). + This masking procedure increases the specificity of alignments and serves to filter out spurious hits. Note that when using --comp-based-stats (2,3,4), tantan masking is disabled by default."> + <option value="0">Disabled</option> + <option value="1" selected="true">Tantan</option> + <option value="seg">SEG</option> + </param> + <conditional name="filter_score"> + <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> + <option value="evalue" selected="True">Maximum e-value to report alignments</option> + <option value="min-score">Minimum bit score to report alignments</option> + </param> + <when value="evalue"> + <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" /> + </when> + <when value="min-score"> + <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" /> + </when> + </conditional> + <param argument="--iterate" type="boolean" truevalue="--iterate" falsevalue="" checked="false" + label="Run multiple rounds of searches with increasing sensitivity" help="he query dataset will first be searched at a lower sensitivity setting, only searching those query sequences at + the target sensitivity that fail to produce a significant alignment at a lower sensitivity." /> + <param argument="--algo" type="select" label="Algorithm for seed search" help="Double-indexed is the main algorithm of the program, designed for large input files but less efficient for small + query files. Query-indexed and improves performance for small query files. This mode will be automatically triggered based on the input. Contiguous-seed mode and further improves performance + for small query files. The modes differ slightly in their sensitivity, so results are not guaranteed to be 100% identical for different settings of this option."> + <option value="0">Doble-indexed (0)</option> + <option value="1">Query-indexed (1)</option> + <option value="ctg">Contiguous-seed mode (ctg)</option> + </param> + <expand macro="hit_filter_macro" /> + <param argument="--global-ranking" type="integer" min="0" value="" optional="true" + label="Limit on the number of Smith Waterman extensions" help="Target sequences will be ranked according to their ungapped extension scores at seed hits, and gapped extensions will only + be computed for the best N targets for each query. Note that this option increases memory use." /> + <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="Report only alignments above the given percentage of sequence identity" /> + <param argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="Report only alignments above the given percentage of query cover" /> + <param argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="Report only alignments above the given percentage of subject cover"/> + <section name="output_section" title="Output options"> + <param argument="--max-hsps" type="integer" min="0" optional="true" label="Maximum number of HSPs" + help="The maximum number of HSPs (High-Scoring Segment Pairs) per target sequence to report for each query. The default policy is to report only the highest-scoring + HSP for each target, while disregarding alternative, lower-scoring HSPs that are contained in the same target." /> + <expand macro="output_type_macro"> + <!-- Taxonomy features are not supported for the DAA format (i.e. + can't be used in diamond view) --> + <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> + <option value="sskingdoms">Subject super kingdoms</option> + <option value="skingdoms">Subject kingdoms</option> + <option value="sphylums">Subject phylums</option> + </expand> + <param name="output_unal" type="select" optional="true" multiple="true" label="Output aligned/unaligned queries to separate file" help=""> + <option value="--un">Output unaligned queries (--un)</option> + <option value="--al">Output alaligned queries (--al)</option> + </param> + </section> + <section name="advanced_section" title="Advanced options" expanded="false"> + <param argument="--seed-cut" type="float" min="0" optional="true" label="Set a complexity cutoff for indexed seeds"/> + <param argument="--freq-masking" type="boolean" truevalue="--freq-masking" falsevalue="" checked="false" label="Enable masking seeds based on frequency" help="This option is incompatible with --sed-cut" /> + <param argument="--motif-masking" type="select" label="Softmask abundant motifs" help="Enable or disable motif masking"> + <option value="0">Disabled</option> + <option value="1">Enabled</option> + </param> + </section> + </inputs> + <outputs> + <expand macro="output_macro" /> + <data format_source="query" name="unalqueries" label="${tool.name} on ${on_string}: unaligned queries"> + <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter> + </data> + <data format_source="query" name="alqueries" label="${tool.name} on ${on_string}: aligned queries"> + <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter> + </data> + </outputs> + <help> +<![CDATA[ + +**What it does** + +DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. +On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting +about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 +times faster than BLASTX, finding more than 94% of all matches. + +The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommended for small datasets. + +.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ + +**Input** + +Input data is a large protein or nucleotide sequence file. + + +**Output** + +Diamond gives you a tabular output file with 12 columns: + +Column Description +1 Query Seq-id (ID of your sequence) +2 Subject Seq-id (ID of the database hit) +3 Percentage of identical matches +4 Alignment length +5 Number of mismatches +6 Number of gap openings +7 Start of alignment in query +8 End of alignment in query +9 Start of alignment in subject (database hit) +10 End of alignment in subject (database hit) +11 Expectation value (E-value) +12 Bit score + + +Supported values for gap open and gap extend parameters depending on the selected scoring matrix. + +======== ============================================ +Matrix Supported values for (gap open)/(gap extend) +======== ============================================ +BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1 +BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1 +BLOSUM62 (6-11)/2; (9-13)/1 +BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1 +BLOSUM90 (6-9)/2; (9-11)/1 +PAM250 (11-15)/3; (13-17)/2; (17-21)/1 +PAM70 (6-8)/2; (9-11)/1 +PAM30 (5-7)/2; (8-10)/1 +======== ============================================ + + +]]> + </help> + <expand macro="citations" /> +</tool>