# HG changeset patch
# User p.lucas
# Date 1718025435 0
# Node ID 4c0effbfd084104202d4f9ce35a92688629cada2
# Parent  f35c3ad107ab211c1bd9ab44006d7655e34b5916
Uploaded

diff -r f35c3ad107ab -r 4c0effbfd084 diamond.xml
--- /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>