| Previous changeset 2:99ff9221182c (2023-11-10) Next changeset 4:bcb50c148f4b (2025-08-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b |
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modified:
macros.xml semibin.xml |
| b |
| diff -r 99ff9221182c -r b5a7583b8db0 macros.xml --- a/macros.xml Fri Nov 10 20:50:01 2023 +0000 +++ b/macros.xml Tue Mar 25 15:55:28 2025 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">2.0.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> <xrefs> @@ -140,9 +140,16 @@ #end for #end if ]]></token> + <xml name="ref_select_cannot"> + <param name="select" type="select" label="Reference database"> + <option value="cached">Cached database</option> + <option value="taxonomy">Pre-computed taxonomy</option> + </param> + </xml> <xml name="ref_select"> <param name="select" type="select" label="Reference database"> - <option value="cached" selected="true">Cached database</option> + <option value="ml" selected="true">Use SemiBin ML function</option> + <option value="cached">Cached database</option> <option value="taxonomy">Pre-computed taxonomy</option> </param> </xml> @@ -153,6 +160,28 @@ </options> </param> </xml> + <xml name="ref-single-cannot"> + <conditional name="ref"> + <expand macro="ref_select_cannot"/> + <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-cannot"> + <conditional name="ref"> + <expand macro="ref_select_cannot"/> + <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"/> @@ -162,6 +191,7 @@ <when value="taxonomy"> <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> </when> + <when value="ml"/> </conditional> </xml> <xml name="ref-multi"> @@ -173,6 +203,7 @@ <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> + <when value="ml"/> </conditional> </xml> <xml name="ref_single"> @@ -184,6 +215,7 @@ <when value="taxonomy"> <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> </when> + <when value="ml"/> </conditional> </xml> <xml name="min_len"> |
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| diff -r 99ff9221182c -r b5a7583b8db0 semibin.xml --- a/semibin.xml Fri Nov 10 20:50:01 2023 +0000 +++ b/semibin.xml Tue Mar 25 15:55:28 2025 +0000 |
| b |
| b'@@ -18,17 +18,19 @@\n #if $mode.select == \'single\' and str($mode.environment) != \'\'\n --environment \'$mode.environment\'\n #end if\n- #if $mode.ref.select == "cached"\n+ #if $mode.ref.select == "cached":\n --reference-db-data-dir \'$mode.ref.cached_db.fields.path\'\n- #else\n+ #end if\n+ #if $mode.ref.select == "taxonomy"\n --taxonomy-annotation-table \'$mode.ref.taxonomy_annotation_table\'\n #end if\n #else\n multi_easy_bin\n --separator \'$separator\'\n- #if $mode.ref.select == "cached"\n+ #if $mode.ref.select == "cached":\n --reference-db-data-dir \'$mode.ref.cached_db.fields.path\'\n- #else\n+ #end if\n+ #if $mode.ref.select == "taxonomy"\n --taxonomy-annotation-table \n #for $e in $mode.ref.taxonomy_annotation_table\n \'$e\' \n@@ -43,7 +45,7 @@\n --orf-finder \'$orf_finder\'\n --random-seed $random_seed\n \n-#if str($annot.ml_threshold) != \'\'\n+#if $annot.ml_threshold:\n --ml-threshold $annot.ml_threshold\n #end if\n --epoches $training.epoches\n@@ -51,7 +53,7 @@\n --max-node $bin.max_node\n --max-edges $bin.max_edges\n --minfasta-kbs $bin.minfasta_kbs\n-#if ($mode.select == \'single\' or $mode.select == \'co\') and "pre_reclustering_bins" in $extra_output\n+#if ($mode.select == \'single\' or $mode.select == \'co\') and $extra_output and "pre_reclustering_bins" in $extra_output\n --write-pre-reclustering-bins\n #end if\n --compression none\n@@ -153,10 +155,58 @@\n <param name="min_len" value="0" />\n </conditional>\n <param name="orf_finder" value="prodigal"/>\n- <param name="random-seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n+ <param name="random_seed" value="0"/>\n+ <section name="training">\n+ <param name="epoches" value="20"/>\n+ <param name="batch_size" value="2048"/>\n+ </section>\n+ <section name="bin">\n+ <param name="max_node" value="1"/>\n+ <param name="max_edges" value="200"/>\n+ <param name="minfasta_kbs" value="200"/>\n </section>\n+ <param name="extra_output" value="data,coverage,contigs"/>\n+ <output_collection name="output_bins" count="0"/>\n+ <output name="single_data" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0"/>\n+ <has_text text="g4k_7"/>\n+ </assert_contents>\n+ </output>\n+ <output name="single_data_split" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0_1"/>\n+ <has_text text="g1k_6_2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="single_cov" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0"/>\n+ <has_text text="0.027"/>\n+ </assert_contents>\n+ </output>\n+ <output name="single_split_cov" ftype="csv">\n+ <assert_contents>\n+ <has_size value="1" delta="1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="5">\n+ <conditional name="mode">\n+ <param name="select" value="single"/>\n+ <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>\n+ <param name="input_bam" ftype="bam" value="input_single.bam"/>\n+ <conditional name="ref">\n+ <param name="select" value="ml"/>\n+ </conditional>\n+ <param name="environment" value="human_gut"/>\n+ </conditional>\n+ <conditional name="min_len">\n+ <param name="method" value="min-len"/>\n+ <param name="min_len" value="0" />\n+ </conditional>\n+ <param name="orf_finder" val'..b'v"/>\n </conditional>\n@@ -207,10 +324,7 @@\n <param name="ratio" value="0.05"/>\n </conditional>\n <param name="orf_finder" value="fast-naive"/>\n- <param name="random-seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n- </section>\n+ <param name="random_seed" value="0"/>\n <section name="training">\n <param name="epoches" value="20"/>\n <param name="batch_size" value="2048"/>\n@@ -278,10 +392,7 @@\n <param name="ratio" value="0.05"/>\n </conditional>\n <param name="orf_finder" value="fraggenescan"/>\n- <param name="random-seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n- </section>\n+ <param name="random_seed" value="0"/>\n <section name="training">\n <param name="epoches" value="20"/>\n <param name="batch_size" value="2048"/>\n@@ -340,7 +451,7 @@\n <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>\n <param name="input_bam" ftype="bam" value="input_single.bam"/>\n <conditional name="ref">\n- <param name="db_selector" value="cached"/>\n+ <param name="select" value="cached"/>\n <param name="cached_db" value="test-db"/>\n </conditional>\n </conditional>\n@@ -349,10 +460,7 @@\n <param name="ratio" value="0.05"/>\n </conditional>\n <param name="orf_finder" value="fraggenescan"/>\n- <param name="random-seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n- </section>\n+ <param name="random_seed" value="0"/>\n <section name="training">\n <param name="epoches" value="20"/>\n <param name="batch_size" value="2048"/>\n@@ -362,7 +470,6 @@\n <param name="max_edges" value="200"/>\n <param name="minfasta_kbs" value="200"/>\n </section>\n- <param name="extra_output" value=""/>\n <output_collection name="output_bins" count="1">\n <element name="SemiBin_30" ftype="fasta">\n <assert_contents>\n@@ -377,7 +484,7 @@\n <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>\n <param name="input_bam" ftype="bam" value="input_single.bam"/>\n <conditional name="ref">\n- <param name="db_selector" value="cached"/>\n+ <param name="select" value="cached"/>\n <param name="cached_db" value="test-db"/>\n </conditional>\n </conditional>\n@@ -386,10 +493,7 @@\n <param name="ratio" value="0.05"/>\n </conditional>\n <param name="orf_finder" value="fraggenescan"/>\n- <param name="random-seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n- </section>\n+ <param name="random_seed" value="0"/>\n <section name="training">\n <param name="epoches" value="20"/>\n <param name="batch_size" value="2048"/>\n@@ -444,9 +548,6 @@\n </conditional>\n <param name="orf_finder" value="fraggenescan"/>\n <param name="random_seed" value="0"/>\n- <section name="annot">\n- <param name="ml_threshold" value=""/>\n- </section>\n <section name="training">\n <param name="epoches" value="20"/>\n <param name="batch_size" value="2048"/>\n@@ -520,4 +621,4 @@\n \n ]]></help>\n <expand macro="citations"/>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |