| Previous changeset 0:7b382efabb98 (2022-10-14) Next changeset 2:99ff9221182c (2023-11-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d |
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modified:
macros.xml semibin.xml |
| b |
| diff -r 7b382efabb98 -r 6b517dc161e4 macros.xml --- a/macros.xml Fri Oct 14 21:38:26 2022 +0000 +++ b/macros.xml Mon Mar 27 08:25:14 2023 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.1.1</token> + <token name="@TOOL_VERSION@">1.5.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> @@ -282,7 +282,7 @@ <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> </data> - <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage"> + <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)"> <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov\.csv" format="csv" directory="output/" /> </collection> @@ -290,7 +290,7 @@ <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov\.csv" format="csv" directory="output/" /> </collection> - <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage"> + <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" /> </collection> @@ -298,11 +298,11 @@ <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> - <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> + <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> </collection> - <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> + <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)"> <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> @@ -348,4 +348,4 @@ <citation type="doi">10.1038/s41467-022-29843-y</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
| b |
| diff -r 7b382efabb98 -r 6b517dc161e4 semibin.xml --- a/semibin.xml Fri Oct 14 21:38:26 2022 +0000 +++ b/semibin.xml Mon Mar 27 08:25:14 2023 +0000 |
| [ |
| b'@@ -110,7 +110,7 @@\n <filter>mode["select"]!="multi"</filter>\n <discover_datasets pattern=".*?\\.(?P<designation>.*).fa" format="fasta" directory="output/output_bins" />\n </collection>\n- <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">\n+ <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">\n <filter>mode["select"]=="multi"</filter>\n <discover_datasets pattern=".*?\\.(?P<designation>.*).fa" format="fasta" directory="output/bins" />\n </collection>\n@@ -158,13 +158,34 @@\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+ <param name="minfasta_kbs" value="2"/>\n <param name="no_recluster" value="false"/>\n </section>\n <param name="extra_output" value="data,coverage,contigs"/>\n- <output_collection name="output_recluster_bins" count="0"/>\n- <output_collection name="output_bins" count="3">\n- <element name="0" ftype="fasta">\n+ <output_collection name="output_recluster_bins" count="39">\n+ \t<element name="0" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">g1k_0"/>\n+ </assert_contents>\n+ </element>\n+ <element name="1" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">g1k_1"/>\n+ </assert_contents>\n+ </element>\n+ <element name="2" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">g1k_2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="39" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">g3k_9"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="output_bins" count="0">\n+ <!--<element name="0" ftype="fasta">\n <assert_contents>\n <has_text text=">g1k_0"/>\n </assert_contents>\n@@ -178,7 +199,7 @@\n <assert_contents>\n <has_text text=">g3k_0"/>\n </assert_contents>\n- </element>\n+ </element>-->\n </output_collection>\n <output name="single_data" ftype="csv">\n <assert_contents>\n@@ -292,6 +313,84 @@\n </element>\n </output_collection>\n </test>\n+ <test expect_num_outputs="4">\n+ <conditional name="mode">\n+ <param name="select" value="co"/>\n+ <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>\n+ <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>\n+ <conditional name="ref">\n+ <param name="select" value="taxonomy"/>\n+ <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>\n+ </conditional>\n+ </conditional>\n+ <conditional name="min_len">\n+ <param name="method" value="ratio"/>\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+ '..b'cov" count="5">\n+ <element name="0" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0"/>\n+ <has_text text="g2k_7"/>\n+ </assert_contents>\n+ </element>\n+ <element name="1" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0"/>\n+ <has_text text="g2k_7"/>\n+ </assert_contents>\n+ </element>\n+ <element name="4" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0"/>\n+ <has_text text="g2k_7"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="co_split_cov" count="5">\n+ <element name="0" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0_1"/>\n+ <has_text text="g2k_7_2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="1" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0_1"/>\n+ <has_text text="g2k_7_2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="2" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0_1"/>\n+ <has_text text="g2k_7_2"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n <test expect_num_outputs="1">\n <conditional name="mode">\n <param name="select" value="single"/>\n@@ -330,6 +429,44 @@\n </element>\n </output_collection>\n </test>\n+ <test expect_num_outputs="2">\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="db_selector" value="cached"/>\n+ <param name="cached_db" value="test-db"/>\n+ </conditional>\n+ </conditional>\n+ <conditional name="min_len">\n+ <param name="method" value="ratio"/>\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+ <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+ <param name="no_recluster" value="false"/>\n+ </section>\n+ <param name="extra_output" value=""/>\n+ <output_collection name="output_recluster_bins" count="1">\n+ <element name="30" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">g3k_0"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n <test expect_num_outputs="8">\n <conditional name="mode">\n <param name="select" value="multi"/>\n@@ -420,6 +557,7 @@\n </element>\n </output_collection>\n </test>\n+ \n </tests>\n <help><![CDATA[\n @HELP_HEADER@\n' |