| Previous changeset 1:43df7a4c33a2 (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 train.xml |
| b |
| diff -r 43df7a4c33a2 -r 8b77643cf479 macros.xml --- a/macros.xml Mon Mar 27 08:26:09 2023 +0000 +++ b/macros.xml Fri Nov 10 20:49:30 2023 +0000 |
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| @@ -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 ${on_string}: Semi-supervised deep learning model" /> |
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| diff -r 43df7a4c33a2 -r 8b77643cf479 train.xml --- a/train.xml Mon Mar 27 08:26:09 2023 +0000 +++ b/train.xml Fri Nov 10 20:49:30 2023 +0000 |
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| @@ -26,14 +26,14 @@ #end if #end for #end if -SemiBin train - --mode '$mode.select' +SemiBin2 train_semi #if $mode.select == 'single' --input-fasta 'contigs.fasta' --data '$mode.data' --data-split '$mode.data_split' --cannot-link '$mode.cannot_link' #else + --train-from-many #for $e in $mode.input_fasta --input-fasta '${e.element_identifier}.fasta' #end for |