Add metawrap (from tools-au)

tools/metawrapmg/.shed.yml

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+---
+categories:
+    - Metagenomics
+description: A flexible pipeline for genome-resolved metagenomic data analysis
+homepage_url: https://github.com/bxlab/metaWRAP
+long_description: |
+    A convenient wrapper around three metagenomic binning software: MaxBin2,
+    metaBAT2, and CONCOCT. Bin refinement utilizes a hybrid approach to take
+    in two or three bin sets that were obtained with different software and
+    produces a consolidated, improved bin set.
+name: metawrapmg_binning
+owner: galaxy-australia
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg
+type: unrestricted

tools/metawrapmg/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.3.0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">22.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">metawrap-mg</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1186/s40168-018-0541-1
+            </citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">metawrap</xref>
+        </xrefs>
+    </xml>
+</macros>

tools/metawrapmg/metawrapmg_binning.xml

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+<tool id="metawrapmg_binning" name="MetaWRAP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description>metagenome binning pipeline</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## set memory usage
+        if [ -n "\${GALAXY_MEMORY_MB}" ] ; then
+            export GALAXY_MEMORY_GB="\$((GALAXY_MEMORY_MB / 1024))" ;
+        fi ;
+
+        ##################
+        ## SET UP FILES ##
+        ##################
+
+        ## only plain FASTA and FASTQ
+        ln -s '$metagenome' metagenome.fasta
+        &&
+        ## Metawrap checks for files named _1.fastq and _2.fastq.
+        ln -s '$input_1' reads_1.fastq
+        &&
+        ln -s '$input_2' reads_2.fastq
+        &&
+
+        #####################
+        ## INITIAL BINNING ##
+        #####################
+
+        metawrap binning 
+        --metabat2 --maxbin2 --concoct 
+        -a metagenome.fasta
+        -m "\${GALAXY_MEMORY_GB:-16}"
+        -o INITIAL_BINNING
+        -t "\${GALAXY_SLOTS:-4}"
+        reads_1.fastq
+        reads_2.fastq
+        &&
+
+        ## Check which binning programs produced bins            
+        bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&
+        switches=('-A' '-B' '-C') &&
+
+        i=0 &&
+        bin_string="" &&
+
+        for dir in "\${bin_dirs[@]}" ; do
+            if [ "\$(find "\$dir" -mindepth 1 -maxdepth 1 -exec echo found \;)" ]; then
+                bin_string+=" \${switches[\$i]} \$dir" ;
+                ((i++)) ;
+            fi
+        done &&
+
+        ####################
+        ## BIN REFINEMENT ##
+        ####################
+
+        ## The checkm database is in the conda package, see
+        ## https://github.com/bioconda/bioconda-recipes/pull/38299.
+
+        metawrap bin_refinement
+        -t "\${GALAXY_SLOTS:-4}"
+        -m "\${GALAXY_MEMORY_GB:-16}"
+        '$hidden_quick'
+        -c '${binning.c}'
+        -x '${binning.x}'
+        -o BIN_REFINEMENT
+        ## Only run bin_refinement on bins with contigs
+        "\${bin_string}"
+    ]]></command>
+    <inputs>
+        <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/>
+        <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1."/>
+        <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2."/>
+        <section name="binning" title="Binning parameters" expanded="false">
+            <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>
+            <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>
+        </section>
+        <!-- the pplacer component requires 40 GB per thread. Skip pplacer for
+         testing by setting this to "quick" -->
+        <param name="hidden_quick" type="hidden" value=""/>
+    </inputs>
+    <outputs>
+        <!-- contigs binned into fasta files -->
+        <collection name="metawrap_bins" type="list" label="MetaWRAP on ${on_string}: bins">
+            <discover_datasets pattern="metawrap_\d+_\d+_bins/(?P&lt;designation&gt;.+)\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true"/>
+        </collection>
+        <!-- summary figures -->
+        <collection name="metawrap_figures" type="list" label="MetaWRAP on ${on_string}: summary figures">
+            <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures"/>
+        </collection>
+        <!-- statistics on binning -->
+        <collection name="metawrap_stats" type="list" label="MetaWRAP on ${on_string}: stat files">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.stats" format="tabular" directory="BIN_REFINEMENT"/>
+        </collection>
+        <!-- which contig went into which bin -->
+        <collection name="metawrap_contigs" type="list" label="MetaWRAP on ${on_string}: contig assignments">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.contigs" format="tabular" directory="BIN_REFINEMENT"/>
+        </collection>
+    </outputs>
+    <tests>
+        <!-- 01: basic function -->
+        <test>
+            <param name="metagenome" value="subset.fasta.gz"/>
+            <param name="input_1" value="mapped_reads.r1.fastq.gz"/>
+            <param name="input_2" value="mapped_reads.r2.fastq.gz"/>
+            <param name="c" value="60"/>
+            <param name="x" value="15"/>
+            <param name="hidden_quick" value="--quick"/>
+            <output_collection name="metawrap_bins" type="list">
+                <element name="bin.1" ftype="fasta">
+                    <assert_contents>
+                        <has_text text="NODE_2_length_"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="metawrap_stats" type="list">
+                <element name="metawrap_60_15_bins" file="test02.stats" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="metawrap_contigs" type="list">
+                <element name="metawrap_60_15_bins" file="test02.contigs" ftype="tabular"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+MetaWRAP
+--------
+
+MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that
+accomplishes the core tasks of metagenomic analysis. Additionally,
+metaWRAP takes bin extraction and analysis to the next level. metaWRAP
+is meant to be a fast and simple approach before you delve deeper into
+parameterization of your analysis. MetaWRAP can be applied to a variety
+of environments, including gut, water, and soil microbiomes (see
+metaWRAP paper for benchmarks).
+
+MetaWRAP binning module
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The metaWRAP::Binning module is meant to be a convenient wrapper around
+three metagenomic binning software: MaxBin2, metaBAT2, and CONCOCT.
+First the metagenomic assembly is indexed with bwa-index, and then
+paired end reads from any number of samples are aligned to it. The
+alignments are sorted and compressed with samtools, and library insert
+size statistics are also gathered at the same time (insert size average
+and standard deviation). metaBAT2’s jgi_summarize_bam_contig_depths
+function is used to generate contig adundance table, and it is then
+converted into the correct format for each of the three binners to take
+as input. After MaxBin2, metaBAT2, and CONCOCT finish binning the
+contigs with default settings, the final bins folders are created with
+formatted bin fasta files. CheckM’s lineage_wf function is used to
+predict essential genes and estimate the completion and contamination of
+each bin.
+
+MetaWRAP bin refinement
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The metaWRAP::Bin_refinement module utilizes a hybrid approach to take
+in two or three bin sets that were obtained with different software and
+produces a consolidated, improved bin set. First, binning_refiner is
+used to create hybridized bins from every possible combination of sets.
+If there were three bin sets: A, B, and C, then the following hybrid
+sets will be produced with binning_refiner: AB, BC, AC, and ABC. CheckM
+is then run to evaluate the completion and contamination of the bins in
+each of the 7 bin sets (3 originals, 4 hybridized). The bins sets are
+then iteratively compared to each other, and each pair is consolidated
+into an improved bin set. To do this, the same bin is identified within
+the two bin sets based on a minimum of 80% overlap in genome length, and
+the better bin is determined based on which bin has the higher score.
+The scoring function is S=Completion-5*Contamination. After all bin sets
+are incorporated into the consolidated bin collection, a de-replication
+function removes any duplicate contigs. If a contig is present in more
+than one bin, it is removed from all but the best bin (based on scoring
+function). CheckM is then run on the final bin set and a final report
+file is generated showing the completion, contamination, and other
+statistics generated by CheckM for each bin. Completion and
+contamination rank plots are also generated to evaluate the success of
+the Bin_refinement module, and compare its output to the quality of the
+original bins.
+
+--------------
+
+MetaWRAP’s home page is
+`bxlab/metaWRAP <https://github.com/bxlab/metaWRAP>`__.
+
+This tool was wrapped by the Galaxy Australia team.
+        ]]></help>
+    <expand macro="citations"/>
+</tool>

tools/metawrapmg/test-data/test02.contigs

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+NODE_2_length_158684_cov_2.789534	bin.1
+NODE_3_length_138621_cov_2.416422	bin.1
+NODE_6_length_106569_cov_3.096156	bin.1
+NODE_7_length_99368_cov_2.860562	bin.1
+NODE_8_length_95669_cov_2.506714	bin.1
+NODE_10_length_88523_cov_2.243252	bin.1
+NODE_11_length_86536_cov_2.926990	bin.1
+NODE_13_length_73331_cov_2.369780	bin.1
+NODE_14_length_72311_cov_2.340345	bin.1
+NODE_15_length_72135_cov_2.745671	bin.1
+NODE_16_length_71859_cov_2.918389	bin.1
+NODE_17_length_70006_cov_2.553159	bin.1
+NODE_24_length_58826_cov_2.290024	bin.1
+NODE_26_length_57188_cov_2.464320	bin.1
+NODE_27_length_54578_cov_2.838857	bin.1
+NODE_30_length_51316_cov_2.828934	bin.1
+NODE_44_length_41143_cov_2.951908	bin.1
+NODE_47_length_40493_cov_2.795440	bin.1
+NODE_49_length_39976_cov_3.111871	bin.1
+NODE_58_length_35924_cov_2.623965	bin.1
+NODE_72_length_33102_cov_2.542954	bin.1
+NODE_89_length_30260_cov_2.967621	bin.1
+NODE_102_length_28495_cov_2.496167	bin.1
+NODE_118_length_26032_cov_2.640605	bin.1
+NODE_119_length_26028_cov_2.951065	bin.1
+NODE_153_length_22539_cov_2.899173	bin.1
+NODE_167_length_21736_cov_2.597805	bin.1
+NODE_229_length_18213_cov_2.462496	bin.1
+NODE_260_length_17127_cov_3.016343	bin.1
+NODE_277_length_16414_cov_2.366465	bin.1
+NODE_370_length_13686_cov_3.065733	bin.1
+NODE_381_length_13339_cov_3.032972	bin.1
+NODE_485_length_11839_cov_2.628564	bin.1
+NODE_502_length_11654_cov_2.455643	bin.1
+NODE_616_length_10584_cov_2.555798	bin.1
+NODE_725_length_9651_cov_2.904023	bin.1
+NODE_1206_length_7144_cov_2.231768	bin.1
+NODE_1409_length_6558_cov_2.842996	bin.1
+NODE_1437_length_6494_cov_3.114769	bin.1
+NODE_1488_length_6399_cov_3.331494	bin.1
+NODE_2109_length_5159_cov_3.299177	bin.1

tools/metawrapmg/test-data/test02.stats

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+bin	completeness	contamination	GC	lineage	N50	size	binner
+bin.1	93.73	0.335	0.406	Clostridiales	70006	1855509	binsAB