Mercurial > repos > iuc > semibin_bin
changeset 5:8317c7dc6407 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
| author | iuc |
|---|---|
| date | Sun, 10 Aug 2025 11:37:53 +0000 |
| parents | 552cfc6ed475 |
| children | |
| files | macros.xml test-data/strobealign_1.txt test-data/strobealign_2.txt test-data/strobealign_3.txt test-data/strobealign_4.txt test-data/strobealign_5.txt |
| diffstat | 6 files changed, 2162 insertions(+), 32 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Fri Aug 01 21:27:15 2025 +0000 +++ b/macros.xml Sun Aug 10 11:37:53 2025 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.0.2</token> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@PROFILE@">24.0</token> + <token name="@TOOL_VERSION@">2.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> <xml name="biotools"> <xrefs> <xref type="bio.tools">semibin</xref> @@ -48,6 +48,23 @@ </when> </conditional> </xml> + <xml name="mode_fasta_strobealign"> + <conditional name="mode"> + <expand macro="mode_select"/> + <when value="single"> + <expand macro="input-fasta-single"/> + <expand macro="input-txt"/> + </when> + <when value="co"> + <expand macro="input-fasta-single"/> + <expand macro="input-txt"/> + </when> + <when value="multi"> + <expand macro="input-fasta-multi"/> + <expand macro="input-txt"/> + </when> + </conditional> + </xml> <xml name="mode_select"> <param name="select" type="select" label="Binning mode"> <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option> @@ -55,6 +72,12 @@ <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option> </param> </xml> + <xml name="bam_or_strobealign"> + <param name="align_select" type="select" label="Use bam or strobealign abundance files?" help="Strobealign abundance files can only be used when samples used in binning above or equal 5"> + <option value="bam">BAM</option> + <option value="txt">Strobealign-aemb file(s)</option> + </param> + </xml> <xml name="input-fasta-single"> <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/> </xml> @@ -129,17 +152,27 @@ <xml name="input-bam-multi"> <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/> </xml> + <!-- Strobealign files --> + <xml name="input-txt"> + <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/> + </xml> <token name="@BAM_FILES@"><![CDATA[ #if $mode.select == 'single' -#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier)) -ln -s '$input_bam' '${identifier}.bam' && +#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.input_bam.element_identifier)) +ln -s '$mode.input_bam' '${identifier}.bam' && #else - #for $e in $input_bam + #for $e in $mode.input_bam #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) ln -s '$e' '${identifier}.bam' && #end for #end if ]]></token> + <token name="@STROBEALIGN_FILES@"><![CDATA[ +#for $e in $mode.align_select.abundance + #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) + ln -s '$e' '${identifier}.txt' && +#end for + ]]></token> <xml name="ref_select_cannot"> <param name="select" type="select" label="Reference database"> <option value="cached">Cached database</option> @@ -257,7 +290,6 @@ <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> <option value="fast-naive" selected="true">Fast-Naive</option> <option value="prodigal">Prodigal</option> - <option value="fraggenescan">Fraggenescan</option> </param> </xml> <xml name="max-node"> @@ -293,58 +325,153 @@ </xml> <xml name="data_output_single"> <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> - <filter>mode["select"]=="single" or mode["select"]=="co"</filter> + <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter> </data> <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data"> - <filter>mode["select"]=="single" or mode["select"]=="co"</filter> + <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter> </data> </xml> - <xml name="data_output_multi"> + <xml name="data_output_multi"> <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample"> - <filter>mode["select"]=="multi"</filter> + <filter>input_type_select['mode']['select']=="multi"</filter> <discover_datasets pattern="(?P<designation>.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample"> - <filter>mode["select"]=="multi"</filter> + <filter>input_type_select['mode']['select']=="multi"</filter> <discover_datasets pattern="(?P<designation>.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> </xml> <xml name="generate_sequence_features_extra_outputs"> <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage"> - <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> </data> <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> - <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> </data> <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)"> - <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov\.csv" format="csv" directory="output/" /> </collection> <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> - <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov\.csv" format="csv" directory="output/" /> </collection> + <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv"> + <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="txt"</filter> + </data> + <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv"> + <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="txt"</filter> + </data> + <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)"> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="txt"</filter> + <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> + </collection> <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)"> - <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> - <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" /> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/> </collection> <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample"> - <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> </collection> <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)"> - <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> </collection> <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)"> - <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter> - <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>input_type_select['input_type']=="bam"</filter> + <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/> </collection> <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs"> - <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> + <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" /> </collection> - + </xml> + <xml name="generate_sequence_features_extra_outputs_main"> + <!-- Single --> + <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage"> + <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter> + </data> + <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)"> + <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter> + </data> + <!-- Bam co aligned --> + <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)"> + <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov\.csv" format="csv" directory="output/" /> + </collection> + <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample"> + <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov\.csv" format="csv" directory="output/" /> + </collection> + + <!-- Bam Multi aligned --> + <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" /> + </collection> + <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern="(?P<designation>.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> + </collection> + <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> + </collection> + <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="bam"</filter> + <discover_datasets pattern=".*\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" /> + </collection> + <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs"> + <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter> + <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" /> + </collection> + <!-- Txt co aligned --> + <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv"> + <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="txt"</filter> + </data> + <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv"> + <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="txt"</filter> + </data> + <!-- Txt multi aligned --> + <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select'] =="txt"</filter> + <discover_datasets pattern="(?P<designation>.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> + </collection> + <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)"> + <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter> + <filter>mode['align_select']</filter> + <filter>mode['align_select']['align_select']=="txt"</filter> + <discover_datasets pattern="(?P<designation>.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/> + </collection> </xml> <xml name="train_output"> <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> @@ -353,31 +480,34 @@ <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" /> </xml> <token name="@HELP_HEADER@"><![CDATA[ + What it does ============ SemiBin is a Semi-supervised siamese neural network for metagenomic binning - -]]></token> + ]]></token> <token name="@HELP_INPUT_FASTA@"><![CDATA[ - Contigs in fasta for 1 or several samples from single or co-assembly -]]></token> + ]]></token> <token name="@HELP_INPUT_BAM@"><![CDATA[ - BAM with reads mapping to the contigs -]]></token> + ]]></token> + <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[ +- TXT alignment files that are the output of strobealign-aemb + ]]></token> <token name="@HELP_CANNOT@"><![CDATA[ - Cannot-link constraints -]]></token> + ]]></token> <token name="@HELP_DATA@"><![CDATA[ - Training data and split training data for the model -]]></token> + ]]></token> <token name="@HELP_MODEL@"><![CDATA[ - Semi-supervised deep learning model -]]></token> + ]]></token> <token name="@HELP_BINS@"><![CDATA[ - Reconstructed bins after reclustering - Reconstructed bins before reclustering -]]></token> + ]]></token> <xml name="citations"> <citations> <citation type="doi">10.1038/s41467-022-29843-y</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strobealign_1.txt Sun Aug 10 11:37:53 2025 +0000 @@ -0,0 +1,400 @@ +S1:g1k_0_1 0.000000 +S1:g1k_0_2 0.000000 +S1:g1k_1_1 0.000000 +S1:g1k_1_2 0.000000 +S1:g1k_2_1 0.000000 +S1:g1k_2_2 0.000000 +S1:g1k_3_1 0.000000 +S1:g1k_3_2 0.000000 +S1:g1k_4_1 0.000000 +S1:g1k_4_2 0.000000 +S1:g1k_5_1 0.000000 +S1:g1k_5_2 0.000000 +S1:g1k_6_1 0.000000 +S1:g1k_6_2 0.000000 +S1:g1k_7_1 0.000000 +S1:g1k_7_2 0.000000 +S1:g1k_8_1 0.000000 +S1:g1k_8_2 0.000000 +S1:g1k_9_1 0.000000 +S1:g1k_9_2 0.000000 +S1:g2k_0_1 0.000000 +S1:g2k_0_2 0.000000 +S1:g2k_1_1 0.000000 +S1:g2k_1_2 0.000000 +S1:g2k_2_1 0.000000 +S1:g2k_2_2 0.000000 +S1:g2k_3_1 0.000000 +S1:g2k_3_2 0.000000 +S1:g2k_4_1 0.000000 +S1:g2k_4_2 0.000000 +S1:g2k_5_1 0.000000 +S1:g2k_5_2 0.000000 +S1:g2k_6_1 0.000000 +S1:g2k_6_2 0.000000 +S1:g2k_7_1 0.000000 +S1:g2k_7_2 0.000000 +S1:g2k_8_1 0.000000 +S1:g2k_8_2 0.000000 +S1:g2k_9_1 0.000000 +S1:g2k_9_2 0.000000 +S2:g1k_0_1 0.000000 +S2:g1k_0_2 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