| Previous changeset 1:6b517dc161e4 (2023-03-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84 |
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modified:
macros.xml semibin.xml |
| b |
| diff -r 6b517dc161e4 -r 99ff9221182c macros.xml --- a/macros.xml Mon Mar 27 08:25:14 2023 +0000 +++ b/macros.xml Fri Nov 10 20:50:01 2023 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.5.1</token> + <token name="@TOOL_VERSION@">2.0.2</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> @@ -15,7 +15,7 @@ </requirements> </xml> <xml name="version"> - <version_command>SemiBin -v</version_command> + <version_command>SemiBin2 -v</version_command> </xml> <xml name="mode_fasta_bam"> <conditional name="mode"> @@ -109,10 +109,11 @@ #end if #end for #set $separator = ':' -SemiBin concatenate_fasta +SemiBin2 concatenate_fasta --input-fasta *.fasta --output 'output' --separator '$separator' + --compression none -m $mode.multi_fasta.min_len && ln -s 'output/concatenated.fa' 'contigs.fasta' && @@ -222,7 +223,8 @@ </xml> <xml name="orf-finder"> <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> - <option value="prodigal" selected="true">Prodigal</option> + <option value="fast-naive" selected="true">Fast-Naive</option> + <option value="prodigal">Prodigal</option> <option value="fraggenescan">Fraggenescan</option> </param> </xml> @@ -251,8 +253,8 @@ <xml name="minfasta-kbs"> <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/> </xml> - <xml name="no-recluster"> - <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/> + <xml name="write_pre_reclustering_bins"> + <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/> </xml> <xml name="data"> <param argument="--data" type="data" format="csv" label="Train data"/> @@ -310,6 +312,7 @@ <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" /> </collection> + </xml> <xml name="train_output"> <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> |
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| diff -r 6b517dc161e4 -r 99ff9221182c semibin.xml --- a/semibin.xml Mon Mar 27 08:25:14 2023 +0000 +++ b/semibin.xml Fri Nov 10 20:50:01 2023 +0000 |
| [ |
| b'@@ -12,8 +12,7 @@\n #import re\n @BAM_FILES@\n @FASTA_FILES@\n-\n-SemiBin\n+SemiBin2\n #if $mode.select == \'single\' or $mode.select == \'co\'\n single_easy_bin\n #if $mode.select == \'single\' and str($mode.environment) != \'\'\n@@ -52,7 +51,10 @@\n --max-node $bin.max_node\n --max-edges $bin.max_edges\n --minfasta-kbs $bin.minfasta_kbs\n- $bin.no_recluster\n+#if ($mode.select == \'single\' or $mode.select == \'co\') and "pre_reclustering_bins" in $extra_output\n+ --write-pre-reclustering-bins\n+#end if\n+ --compression none\n --threads \\${GALAXY_SLOTS:-1}\n --processes \\${GALAXY_SLOTS:-1}\n && \n@@ -93,26 +95,30 @@\n <expand macro="max-node"/>\n <expand macro="max-edges"/>\n <expand macro="minfasta-kbs"/>\n- <expand macro="no-recluster"/>\n </section>\n <param name="extra_output" type="select" multiple="true" optional="true" label="Extra outputs" help="In addition to the training data">\n <option value="data">Training data</option>\n <option value="coverage">Coverage files</option>\n <option value="contigs">Contigs (if multiple sample)</option>\n+ <option value="pre_reclustering_bins">Pre-reclustering bins (only single sample and co-assembly)</option>\n </param>\n </inputs>\n <outputs>\n- <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">\n- <filter>not bin["no_recluster"]</filter>\n- <discover_datasets pattern=".*?\\.(?P<designation>.*).fa" format="fasta" directory="output/output_recluster_bins" />\n+ <collection name="output_pre_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">\n+ <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_prerecluster_bins"/>\n </collection>\n- <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">\n- <filter>mode["select"]!="multi"</filter>\n- <discover_datasets pattern=".*?\\.(?P<designation>.*).fa" format="fasta" directory="output/output_bins" />\n+ <collection name="output_after_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">\n+ <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_recluster_bins"/>\n+ </collection>\n+ <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins">\n+ <filter>mode["select"]!="multi" and not "pre_reclustering_bins" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_bins"/>\n </collection>\n <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">\n <filter>mode["select"]=="multi"</filter>\n- <discover_datasets pattern=".*?\\.(?P<designation>.*).fa" format="fasta" directory="output/bins" />\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/bins"/>\n </collection>\n <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">\n <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>\n@@ -131,7 +137,7 @@\n <expand macro="generate_sequence_features_extra_outputs"/>\n </outputs>\n <tests>\n- <test expect_num_outputs="'..b'bins" count="3">\n- <element name="0" ftype="fasta">\n+ <output_collection name="output_bins" count="1">\n+ <element name="SemiBin_30" ftype="fasta">\n <assert_contents>\n- <has_text text=">g1k_0"/>\n+ <has_text text=">g3k_0"/>\n </assert_contents>\n </element>\n </output_collection>\n@@ -456,13 +398,29 @@\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+ <param name="extra_output" value="pre_reclustering_bins"/>\n+ <output_collection name="output_pre_recluster_bins" count="3">\n+ <element name="SemiBin_0" ftype="fasta">\n+ <assert_contents> \n+ <has_text text="g1k_0"/>\n+ </assert_contents>\n+ </element>\n+ <element name="SemiBin_1" ftype="fasta">\n+ <assert_contents> \n+ <has_text text="g2k_0"/>\n+ </assert_contents>\n+ </element>\n+ <element name="SemiBin_2" ftype="fasta">\n+ <assert_contents> \n+ <has_text text="g3k_0"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="output_after_recluster_bins" count="1">\n+ <element name="SemiBin_30" ftype="fasta">\n <assert_contents>\n- <has_text text=">g3k_0"/>\n+ <has_text text="g3k_0"/>\n </assert_contents>\n </element>\n </output_collection>\n@@ -497,23 +455,9 @@\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="true"/>\n </section>\n <param name="extra_output" value="data,coverage,contigs"/>\n- <output_collection name="multi_bins" count="2">\n- <element name="0" ftype="fasta">\n- <assert_contents>\n- <has_text text=">g1k_0"/>\n- </assert_contents>\n- </element>\n- </output_collection>\n- <output_collection name="multi_contigs" count="10">\n- <element name="S8" ftype="fasta">\n- <assert_contents>\n- <has_text text=">g1k_0"/>\n- </assert_contents>\n- </element>\n- </output_collection>\n+ <output_collection name="multi_bins" count="0"/>\n <output_collection name="multi_data" count="10">\n <element name="S8" ftype="csv">\n <assert_contents>\n@@ -521,6 +465,13 @@\n </assert_contents>\n </element>\n </output_collection>\n+ <output_collection name="multi_data_split" count="10">\n+ <element name="S8" ftype="csv">\n+ <assert_contents>\n+ <has_text text="g1k_0_1,"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n <output_collection name="multi_cov" count="10">\n <element name="8" ftype="csv">\n <assert_contents>\n@@ -557,7 +508,6 @@\n </element>\n </output_collection>\n </test>\n- \n </tests>\n <help><![CDATA[\n @HELP_HEADER@\n' |