Mercurial > repos > iuc > semibin_concatenate_fasta
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
author | iuc |
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date | Fri, 14 Oct 2022 21:51:40 +0000 |
parents | |
children | e6bc3455940e |
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<?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.1.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> <xrefs> <xref type="bio.tools">semibin</xref> </xrefs> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">semibin</requirement> <yield/> </requirements> </xml> <xml name="version"> <version_command>SemiBin -v</version_command> </xml> <xml name="mode_fasta_bam"> <conditional name="mode"> <expand macro="mode_select"/> <when value="single"> <expand macro="input-fasta-single"/> <expand macro="input-bam-single"/> </when> <when value="co"> <expand macro="input-fasta-single"/> <expand macro="input-bam-multi"/> </when> <when value="multi"> <expand macro="input-fasta-multi"/> <expand macro="input-bam-multi"/> </when> </conditional> </xml> <xml name="mode_fasta"> <conditional name="mode"> <expand macro="mode_select"/> <when value="single"> <expand macro="input-fasta-single"/> </when> <when value="co"> <expand macro="input-fasta-single"/> </when> <when value="multi"> <expand macro="input-fasta-multi"/> </when> </conditional> </xml> <xml name="mode_select"> <param name="select" type="select" label="Binning mode"> <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option> <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option> <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option> </param> </xml> <xml name="input-fasta-single"> <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/> </xml> <xml name="input-fasta-multi"> <conditional name="multi_fasta"> <param name="select" type="select" label="Contig files of the samples"> <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option> <option value="multi">1 contig file per sample</option> </param> <when value="concatenated"> <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/> <expand macro="separator"/> </when> <when value="multi"> <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/> <expand macro="concat_min_len"/> </when> </conditional> </xml> <xml name="concat_min_len"> <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/> </xml> <token name="@SINGLE_FASTA_FILES@"><![CDATA[ #if $input_fasta.ext.endswith(".gz") gunzip -c '$input_fasta' > 'contigs.fasta' && #else ln -s '$input_fasta' 'contigs.fasta' && #end if ]]></token> <token name="@FASTA_FILES@"><![CDATA[ #if $mode.select == 'single' or $mode.select == 'co' #if $mode.input_fasta.ext.endswith(".gz") gunzip -c '$mode.input_fasta' > 'contigs.fasta' && #else ln -s '$mode.input_fasta' 'contigs.fasta' && #end if #else #if $mode.multi_fasta.select == 'concatenated' #if $mode.multi_fasta.input_fasta.ext.endswith(".gz") gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' && #else ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' && #end if #set $separator = $mode.multi_fasta.separator #else #for $e in $mode.multi_fasta.input_fasta #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) #if $e.ext.endswith(".gz") gunzip -c '$e' > '${identifier}.fasta' && #else ln -s '$e' '${identifier}.fasta' && #end if #end for #set $separator = ':' SemiBin concatenate_fasta --input-fasta *.fasta --output 'output' --separator '$separator' -m $mode.multi_fasta.min_len && ln -s 'output/concatenated.fa' 'contigs.fasta' && #end if #end if ]]></token> <xml name="separator"> <param argument="--separator" type="text" value=":" label="Separator in the contig file between sample name and contig name"/> </xml> <xml name="input-bam-single"> <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/> </xml> <xml name="input-bam-multi"> <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/> </xml> <token name="@BAM_FILES@"><![CDATA[ #if $mode.select == 'single' #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier)) ln -s '$input_bam' '${identifier}.bam' && #else #for $e in $input_bam #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) ln -s '$e' '${identifier}.bam' && #end for #end if ]]></token> <xml name="ref_select"> <param name="select" type="select" label="Reference database"> <option value="cached" selected="true">Cached database</option> <option value="taxonomy">Pre-computed taxonomy</option> </param> </xml> <xml name="cached_db"> <param name="cached_db" label="Cached databases" type="select"> <options from_data_table="gtdb"> <validator message="No GTDB database is available" type="no_options" /> </options> </param> </xml> <xml name="ref-single"> <conditional name="ref"> <expand macro="ref_select"/> <when value="cached"> <expand macro="cached_db"/> </when> <when value="taxonomy"> <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> </when> </conditional> </xml> <xml name="ref-multi"> <conditional name="ref"> <expand macro="ref_select"/> <when value="cached"> <expand macro="cached_db"/> </when> <when value="taxonomy"> <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/> </when> </conditional> </xml> <xml name="ref_single"> <conditional name="ref"> <expand macro="ref_select"/> <when value="cached"> <expand macro="cached_db"/> </when> <when value="taxonomy"> <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> </when> </conditional> </xml> <xml name="min_len"> <conditional name="min_len"> <param name="method" type="select" label="Method to set up the minimal length for contigs in binning"> <option value="automatic">Automatic</option> <option value="min-len">Manual</option> <option value="ratio">Computation based on ratio of the number of base pairs</option> </param> <when value="automatic"/> <when value="min-len"> <param argument="--min-len" type="integer" min="0" value="0" label="Minimal length for contigs in binning"/> </when> <when value="ratio"> <param argument="--ratio" type="float" min="0" max="1" value="0.05" label="Ratio of the number of base pairs of contigs between 1000-2500 bp below which the minimal length will be set as 1000bp, otherwise 2500bp."/> </when> </conditional> </xml> <token name="@MIN_LEN@"><![CDATA[ #if $min_len.method == 'min-len' --min-len $min_len.min_len #else if $min_len.method == 'ratio' --ratio $min_len.ratio #end if ]]></token> <xml name="random-seed"> <param argument="--random-seed" type="integer" min="0" value="0" label="Random seed to reproduce result"/> </xml> <xml name="ml-threshold"> <param argument="--ml-threshold" type="integer" min="0" value="" optional="true" label="Length threshold for generating must-link constraints" help="If no value is given, the threshold is calculated from the contig, and the default minimum value is 4,000 bp."/> </xml> <xml name="epoches"> <param argument="--epoches" type="integer" min="0" value="20" label="Number of epoches used in the training process"/> </xml> <xml name="batch-size"> <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/> </xml> <xml name="orf-finder"> <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> <option value="prodigal" selected="true">Prodigal</option> <option value="fraggenescan">Fraggenescan</option> </param> </xml> <xml name="max-node"> <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/> </xml> <xml name="max-edges"> <param argument="--max-edges" type="integer" min="0" value="200" label="Maximum number of edges that can be connected to one contig"/> </xml> <xml name="environment"> <param argument="--environment" type="select" optional="true" label="Environment for the built-in model"> <option value="" selected="true">None</option> <option value="human_gut">Human gut</option> <option value="dog_gut">Dog gut</option> <option value="ocean">Ocean</option> <option value="soil">Soil</option> <option value="cat_gut">Cat gut</option> <option value="human_oral">Human oral</option> <option value="mouse_gut">Mouse gut</option> <option value="pig_gut">Pig gut</option> <option value="built_environment">Built environment</option> <option value="wastewater">Wastewater</option> <option value="global">Global</option> </param> </xml> <xml name="minfasta-kbs"> <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/> </xml> <xml name="no-recluster"> <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/> </xml> <xml name="data"> <param argument="--data" type="data" format="csv" label="Train data"/> </xml> <xml name="data_output_single"> <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> <filter>mode["select"]=="single" or mode["select"]=="co"</filter> </data> <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data"> <filter>mode["select"]=="single" or mode["select"]=="co"</filter> </data> </xml> <xml name="data_output_multi"> <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample"> <filter>mode["select"]=="multi"</filter> <discover_datasets pattern="(?P<designation>.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample"> <filter>mode["select"]=="multi"</filter> <discover_datasets pattern="(?P<designation>.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> </xml> <xml name="generate_sequence_features_extra_outputs"> <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage"> <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> </data> <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> </data> <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage"> <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov\.csv" format="csv" directory="output/" /> </collection> <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov\.csv" format="csv" directory="output/" /> </collection> <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" /> </collection> <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> </collection> <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs"> <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" /> </collection> </xml> <xml name="train_output"> <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> </xml> <xml name="cannot_link_output"> <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" /> </xml> <token name="@HELP_HEADER@"><![CDATA[ What it does ============ SemiBin is a Semi-supervised siamese neural network for metagenomic binning ]]></token> <token name="@HELP_INPUT_FASTA@"><![CDATA[ - Contigs in fasta for 1 or several samples from single or co-assembly ]]></token> <token name="@HELP_INPUT_BAM@"><![CDATA[ - BAM with reads mapping to the contigs ]]></token> <token name="@HELP_CANNOT@"><![CDATA[ - Cannot-link constraints ]]></token> <token name="@HELP_DATA@"><![CDATA[ - Training data and split training data for the model ]]></token> <token name="@HELP_MODEL@"><![CDATA[ - Semi-supervised deep learning model ]]></token> <token name="@HELP_BINS@"><![CDATA[ - Reconstructed bins after reclustering - Reconstructed bins before reclustering ]]></token> <xml name="citations"> <citations> <citation type="doi">10.1038/s41467-022-29843-y</citation> </citations> </xml> </macros>