diff --git a/tools/metawrapmg/.shed.yml b/tools/metawrapmg/.shed.yml
deleted file mode 100644
index c46ca480..00000000
--- a/tools/metawrapmg/.shed.yml
+++ /dev/null
@@ -1,19 +0,0 @@
----
-categories:
-    - Metagenomics
-description: A flexible pipeline for genome-resolved metagenomic data analysis
-exclude:
-    - extras
-    - README.md
-    - tool_test_output.html
-    - tool_test_output.json
-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/usegalaxy-au/tools-au/tree/master/tools/metawrapmg
-type: unrestricted
diff --git a/tools/metawrapmg/README.md b/tools/metawrapmg/README.md
new file mode 100644
index 00000000..031f879b
--- /dev/null
+++ b/tools/metawrapmg/README.md
@@ -0,0 +1,7 @@
+# MetaWrap binning
+
+The MetaWrap binning wrapper for Galaxy has been
+[moved](https://github.com/galaxyproject/tools-iuc/pull/5936) to
+[galaxyproject/tools-iuc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg).
+
+The Snakemake workflow under `extras/` was not included in the move.
diff --git a/tools/metawrapmg/macros.xml b/tools/metawrapmg/macros.xml
deleted file mode 100644
index f05e03e7..00000000
--- a/tools/metawrapmg/macros.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<macros>
-    <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">0</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>
diff --git a/tools/metawrapmg/metawrapmg_binning.xml b/tools/metawrapmg/metawrapmg_binning.xml
deleted file mode 100644
index 847703fb..00000000
--- a/tools/metawrapmg/metawrapmg_binning.xml
+++ /dev/null
@@ -1,189 +0,0 @@
-<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
-                GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
-            fi ;
-
-            ##################
-            ## SET UP FILES ##
-            ##################
-
-            ## should always be FASTA
-            #set mg_fn = 'metagenome.' + str($metagenome.ext)
-            ln -s '$metagenome' $mg_fn
-            &&
-
-            ## Only FASTQ. Separate files for each sample. Metawrap checks for
-            ## files named _1.fastq and _2.fastq.
-            #set input1_fn = 'reads_1.fastq'
-            ln -s '$input_1' $input1_fn
-            &&
-
-            #set input2_fn = 'reads_2.fastq'
-            ln -s '$input_2' $input2_fn
-            &&
-
-            #####################
-            ## INITIAL BINNING ##
-            #####################
-
-            metawrap binning 
-            --metabat2 --maxbin2 --concoct 
-            -a '$mg_fn'
-            -m \${GALAXY_MEMORY_GB:-16}
-            -o INITIAL_BINNING
-            -t \${GALAXY_SLOTS:-4}
-            '$input1_fn'
-            '$input2_fn'
-            &&
-
-            ## 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 | read; then
-                    bin_string="\${bin_string} \${switches[\$i]} \${dir}" ;
-                    i+=1 ;
-                fi
-            done &&
-
-            ####################
-            ## BIN REFINEMENT ##
-            ####################
-
-            ## The checkm database is included in the conda package.
-            ## Requires metawrap-mg_1.3.0--hdfd78af_1 or later. See
-            ## https://github.com/bioconda/bioconda-recipes/pull/38299.
-
-            metawrap bin_refinement
-            -t \${GALAXY_SLOTS:-4}
-            -m \${GALAXY_MEMORY_GB:-16}
-            -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>
-    </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" visible="false" />
-        </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" visible="false" />
-        </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" visible="false" />
-        </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" visible="false" />
-        </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"/>
-            <!-- this is the main output, but it's too large to test -->
-            <!-- <output_collection name="metawrap_bins" type="list">
-                <element name="bin.1" file="test02.fa" ftype="fasta"/>
-            </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>
diff --git a/tools/metawrapmg/test-data/mapped_reads.r1.fastq.gz b/tools/metawrapmg/test-data/mapped_reads.r1.fastq.gz
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index bc702a95..00000000
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diff --git a/tools/metawrapmg/test-data/mapped_reads.r2.fastq.gz b/tools/metawrapmg/test-data/mapped_reads.r2.fastq.gz
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index 0baa837f..00000000
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diff --git a/tools/metawrapmg/test-data/subset.fasta.gz b/tools/metawrapmg/test-data/subset.fasta.gz
deleted file mode 100644
index 740d1581..00000000
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diff --git a/tools/metawrapmg/test-data/test02.contigs b/tools/metawrapmg/test-data/test02.contigs
deleted file mode 100644
index aecee72e..00000000
--- a/tools/metawrapmg/test-data/test02.contigs
+++ /dev/null
@@ -1,41 +0,0 @@
-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
diff --git a/tools/metawrapmg/test-data/test02.stats b/tools/metawrapmg/test-data/test02.stats
deleted file mode 100644
index 3d58a013..00000000
--- a/tools/metawrapmg/test-data/test02.stats
+++ /dev/null
@@ -1,2 +0,0 @@
-bin	completeness	contamination	GC	lineage	N50	size	binner
-bin.1	93.73	0.335	0.406	Clostridiales	70006	1855509	binsAB