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Add Galaxy wrapper for motus map_snv (#1796)
* Added map snv * Fix map_snv. Modified version and profile in merge and profile * Updated macros.xml * Updated .shed.yml
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‎tools/motus/.shed.yml‎

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mOTUs is a tool designed for profiling the abundance of microbial taxa in metagenomic datasets.
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It can identify and quantify microbial taxa in samples, providing valuable insights into microbial community composition.
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The tool works by analyzing metagenomic reads, offering high-resolution taxonomic profiling, and is particularly useful for microbial ecology studies and microbiome research.
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/motus
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categories:
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- Metagenomics

‎tools/motus/macros.xml‎

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</xrefs>
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</xml>
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<token name="@TOOL_VERSION@">3.1.0</token>
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<token name="@VERSION_SUFFIX@">galaxy0</token>
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<token name="@PROFILE@">21.05</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@COMPATIBLE_MOTUSDB_VERSION@">3.1.0</token>
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<xml name="citations">
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<citations>

‎tools/motus/motus_map_snv.xml‎

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<tool id="motus_map_snv" name="Map SNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>Map reads to the marker gene database for SNV calling</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="biotools"/>
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<expand macro="requirements"/>
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<command detect_errors="exit_code"><![CDATA[
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#if $db.db_source == 'cached'
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#set $DATABASE_DIR=$db.db_cached.fields.path
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#else
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#set $database_path = $db.database
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mkdir database_dir &&
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tar -xvf '$database_path' -C database_dir/ &&
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#set $DATABASE_DIR = 'database_dir/db_mOTU' ##the actual DB folder in the archive called db_mOTU
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#end if
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echo "Database Directory:" $DATABASE_DIR &&
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motus map_snv
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#if $inputs.reads_type.selector == 'paired'
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-f '${inputs.reads_type.forward_reads}'
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-r '${inputs.reads_type.reverse_reads}'
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#elif $inputs.reads_type.selector == 'single'
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-s '${inputs.reads_type.unpaired_reads}'
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#end if
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-db '$DATABASE_DIR'
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-l $algorithm_advanced_options.minimum_alignment_len
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-v $algorithm_advanced_options.verbosity_level_selection
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-o '$bam_output'
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]]></command>
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<inputs>
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<section name="inputs" title="Inputs" expanded="true">
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<conditional name="reads_type">
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<param name="selector" type="select" format="fastq,fastq.gz" label="Choose input file(s)">
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<option value="paired">Paired-end</option>
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<option value="single" selected="true">Single</option>
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</param>
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<when value="paired">
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<param name="forward_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="-f Input file(s) for reads in forward orientation, fastq(.gz)-formatted"/>
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<param name="reverse_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="-r Input file(s) for reads in reverse orientation, fastq(.gz)-formatted"/>
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</when>
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<when value="single">
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<param name="unpaired_reads" type="data" format="fastq,fastq.gz" label="Single reads" help="-s input file(s) for single reads, fastq(.gz)-formatted"/>
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</when>
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</conditional>
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<conditional name="db">
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<param name="db_source" type="select" label="mOTUs Database">
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<option value="cached" selected="True">Use a pre-installed database</option>
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<option value="history">Use a database from history</option>
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</param>
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<when value="cached">
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<param name="db_cached" type="select" label="A pre-installed mOTUs databese" help="no pre-installed mOTUs databases are avalable yet">
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<options from_data_table="motus_db_versioned">
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<filter type="sort_by" column="1"/>
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<validator type="no_options" message="No compatible motus database is available"/>
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</options>
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</param>
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</when>
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<when value="history">
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<param name="database" type="data" format="tar" label="Database from history" help="Custom database or other version of mOTUs database from link: https://zenodo.org/records/5140350"/>
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</when>
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</conditional>
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</section>
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<section name="algorithm_advanced_options" title="Advanced Options" expanded="true">
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<param argument="-v" name="verbosity_level_selection" type="select" label="verbosity level" help="-v verbosity level">
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<option value="1">error</option>
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<option value="2">warning</option>
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<option value="3" selected="True">message default</option>
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<option value="4">debugging</option>
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</param>
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<param argument="-l" name="minimum_alignment_len" type="integer" value="75" optional="true" label="Minimum Alignment Length (bp)" help="Specify the desired minimum alignment length in base pairs. Default value is 75bp."/>
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</section>
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</inputs>
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<outputs>
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<data name="bam_output" format="bam" label="${tool.name} on ${on_string}: mapped reads"/>
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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<section name="inputs">
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<conditional name="reads_type">
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<param name="selector" value="single"/>
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<param name="unpaired_reads" ftype="fastq.gz" value="test1_single.fastq"/>
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</conditional>
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<conditional name="db">
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<param name="db_source" value="history"/>
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<param name="database" location="https://zenodo.org/record/7778108/files/db_mOTU_v3.1.0.tar.gz"/>
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</conditional>
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</section>
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<output name="bam_output" ftype="bam">
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<assert_contents>
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<has_size value="7133479" delta="1000"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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What it does
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============
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The mOTUs Map SNV tool maps metagenomic reads to the marker gene database for single nucleotide variant (SNV) calling.
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This is the first step in the mOTUs SNV analysis pipeline, preparing read alignments for subsequent variant detection with 'snv_call'.
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]]></help>
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<expand macro="citations"/>
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</tool>

‎tools/motus/motus_merge.xml‎

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<tool id="mereg_mOTUs_tables" name="Merge" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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<tool id="mereg_mOTUs_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>Merge mOTUs aboundance or count tables</description>
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<macros>
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<import>macros.xml</import>

‎tools/motus/motus_profiler.xml‎

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<tool id="motus_profiler" name="mOTUs_profiler" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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<tool id="motus_profiler" name="mOTUs_profiler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>performs taxonomic profiling of metagenomics and metatrancriptomics samples</description>
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<macros>
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<import>macros.xml</import>

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