| Previous changeset 1:e3a64a1d2a6e (2023-01-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 26fe7d23c5c3981c9b737109e5db799cc5d23932 |
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modified:
macros.xml metawrapmg_binning.xml |
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| diff -r e3a64a1d2a6e -r 2a8bc1d26d06 macros.xml --- a/macros.xml Mon Jan 30 22:30:51 2023 +0000 +++ b/macros.xml Thu Apr 11 21:56:14 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> |
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| diff -r e3a64a1d2a6e -r 2a8bc1d26d06 metawrapmg_binning.xml --- a/metawrapmg_binning.xml Mon Jan 30 22:30:51 2023 +0000 +++ b/metawrapmg_binning.xml Thu Apr 11 21:56:14 2024 +0000 |
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| b'@@ -6,100 +6,97 @@\n <expand macro="xrefs"/>\n <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n- ## set memory usage\n- if [ -n "\\$GALAXY_MEMORY_MB" ] ; then\n- GALAXY_MEMORY_GB=\\$((GALAXY_MEMORY_MB / 1024)) ;\n- fi ;\n+ ## set memory usage\n+ if [ -n "\\${GALAXY_MEMORY_MB}" ] ; then\n+ export GALAXY_MEMORY_GB="\\$((GALAXY_MEMORY_MB / 1024))" ;\n+ fi ;\n \n- ##################\n- ## SET UP FILES ##\n- ##################\n-\n- ## should always be FASTA\n- #set mg_fn = \'metagenome.\' + str($metagenome.ext)\n- ln -s \'$metagenome\' $mg_fn\n- &&\n+ ##################\n+ ## SET UP FILES ##\n+ ##################\n \n- ## Only FASTQ. Separate files for each sample. Metawrap checks for\n- ## files named _1.fastq and _2.fastq.\n- #set input1_fn = \'reads_1.fastq\'\n- ln -s \'$input_1\' $input1_fn\n- &&\n+ ## only plain FASTA and FASTQ\n+ ln -s \'$metagenome\' metagenome.fasta\n+ &&\n+ ## Metawrap checks for files named _1.fastq and _2.fastq.\n+ ln -s \'$input_1\' reads_1.fastq\n+ &&\n+ ln -s \'$input_2\' reads_2.fastq\n+ &&\n \n- #set input2_fn = \'reads_2.fastq\'\n- ln -s \'$input_2\' $input2_fn\n- &&\n-\n- #####################\n- ## INITIAL BINNING ##\n- #####################\n+ #####################\n+ ## INITIAL BINNING ##\n+ #####################\n \n- metawrap binning \n- --metabat2 --maxbin2 --concoct \n- -a \'$mg_fn\'\n- -m \\${GALAXY_MEMORY_GB:-16}\n- -o INITIAL_BINNING\n- -t \\${GALAXY_SLOTS:-4}\n- \'$input1_fn\'\n- \'$input2_fn\'\n- &&\n+ metawrap binning \n+ --metabat2 --maxbin2 --concoct \n+ -a metagenome.fasta\n+ -m "\\${GALAXY_MEMORY_GB:-16}"\n+ -o INITIAL_BINNING\n+ -t "\\${GALAXY_SLOTS:-4}"\n+ reads_1.fastq\n+ reads_2.fastq\n+ &&\n \n- ## Check which binning programs produced bins \n- bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&\n- switches=(\'-A\' \'-B\' \'-C\') &&\n+ ## Check which binning programs produced bins \n+ bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&\n+ switches=(\'-A\' \'-B\' \'-C\') &&\n \n- i=0 &&\n- bin_string="" &&\n+ i=0 &&\n+ bin_string="" &&\n \n- for dir in "\\${bin_dirs[@]}" ; do\n- if find "\\${dir}" -mindepth 1 -maxdepth 1 | read; then\n- bin_string="\\${bin_string} \\${switches[\\$i]} \\${dir}" ;\n- i+=1 ;\n- fi\n- done &&\n+ for dir in "\\${bin_dirs[@]}" ; do\n+ if [ "\\$(find "\\$dir" -mindepth 1 -maxdepth 1 -exec echo found \\;)" ]; then\n+ bin_string+=" \\${switches[\\$i]} \\$dir" ;\n+ ((i++)) ;\n+ fi\n+ done &&\n \n- ####################\n- ## BIN REFINEMENT ##\n- ####################\n+ ####################\n+ ## BIN REFINEMENT ##\n+ ####################\n \n- ## The checkm database is included in the conda package.\n- ## Requires metawrap-mg_1.3.0--hdfd78af_1 or later. See\n- ## https://github.com/bioconda/bioconda-recipes/pull/38299.\n+ ## The checkm database is in the conda package, see\n+ ## https://github.com/bioconda/bioconda-recipes/pull/38299.\n \n- metawrap bin_refinement\n- -t \\${GALAXY_SLOTS:-4}\n- -m \\${GALAXY_MEMORY_GB:-16}\n- -c $binning.c\n- -x $binning.x\n- -o BIN_REFINEMENT\n- ## Only run bin_refinement on bins wit'..b' 2" help="Original reads that were used for the assembly: read 2."/>\n <section name="binning" title="Binning parameters" expanded="false">\n- <param argument=\'-c\' type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins" />\n- <param argument=\'-x\' type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable" />\n+ <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>\n+ <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>\n </section>\n+ <!-- the pplacer component requires 40 GB per thread. Skip pplacer for\n+ testing by setting this to "quick" -->\n+ <param name="hidden_quick" type="hidden" value=""/>\n </inputs>\n <outputs>\n <!-- contigs binned into fasta files -->\n <collection name="metawrap_bins" type="list" label="MetaWRAP on ${on_string}: bins">\n- <discover_datasets pattern="metawrap_\\d+_\\d+_bins/(?P<designation>.+)\\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true" visible="false" />\n+ <discover_datasets pattern="metawrap_\\d+_\\d+_bins/(?P<designation>.+)\\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true"/>\n </collection>\n <!-- summary figures -->\n <collection name="metawrap_figures" type="list" label="MetaWRAP on ${on_string}: summary figures">\n- <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures" visible="false" />\n+ <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures"/>\n </collection>\n <!-- statistics on binning -->\n <collection name="metawrap_stats" type="list" label="MetaWRAP on ${on_string}: stat files">\n- <discover_datasets pattern="(?P<designation>.+)\\.stats" format="tabular" directory="BIN_REFINEMENT" visible="false" />\n+ <discover_datasets pattern="(?P<designation>.+)\\.stats" format="tabular" directory="BIN_REFINEMENT"/>\n </collection>\n <!-- which contig went into which bin -->\n <collection name="metawrap_contigs" type="list" label="MetaWRAP on ${on_string}: contig assignments">\n- <discover_datasets pattern="(?P<designation>.+)\\.contigs" format="tabular" directory="BIN_REFINEMENT" visible="false" />\n+ <discover_datasets pattern="(?P<designation>.+)\\.contigs" format="tabular" directory="BIN_REFINEMENT"/>\n </collection>\n </outputs>\n <tests>\n@@ -110,10 +107,14 @@\n <param name="input_2" value="mapped_reads.r2.fastq.gz"/>\n <param name="c" value="60"/>\n <param name="x" value="15"/>\n- <!-- this is the main output, but it\'s too large to test -->\n- <!-- <output_collection name="metawrap_bins" type="list">\n- <element name="bin.1" file="test02.fa" ftype="fasta"/>\n- </output_collection> -->\n+ <param name="hidden_quick" value="--quick"/>\n+ <output_collection name="metawrap_bins" type="list">\n+ <element name="bin.1" ftype="fasta">\n+ <assert_contents>\n+ <has_text text="NODE_2_length_"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n <output_collection name="metawrap_stats" type="list">\n <element name="metawrap_60_15_bins" file="test02.stats" ftype="tabular"/>\n </output_collection>\n@@ -122,7 +123,7 @@\n </output_collection>\n </test>\n </tests>\n- <help><![CDATA[\n+ <help><![CDATA[\n MetaWRAP\n --------\n \n' |