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Changeset 5:8317c7dc6407 (2025-08-10)

Previous changeset 4:552cfc6ed475 (2025-08-01) Next changeset 6:8428eb03a349 (2025-10-28)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7

modified:
macros.xml

added:
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

diff -r 552cfc6ed475 -r 8317c7dc6407 macros.xml
--- a/macros.xml Fri Aug 01 21:27:15 2025 +0000
+++ b/macros.xml Sun Aug 10 11:37:53 2025 +0000

[

b'@@ -1,8 +1,8 @@\n <?xml version="1.0"?>\n <macros>\n- <token name="@TOOL_VERSION@">2.0.2</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n- <token name="@PROFILE@">24.0</token>\n+ <token name="@TOOL_VERSION@">2.1.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">21.01</token>\n <xml name="biotools">\n <xrefs>\n <xref type="bio.tools">semibin</xref>\n@@ -48,6 +48,23 @@\n </when>\n </conditional>\n </xml>\n+ <xml name="mode_fasta_strobealign">\n+ <conditional name="mode">\n+ <expand macro="mode_select"/>\n+ <when value="single">\n+ <expand macro="input-fasta-single"/>\n+ <expand macro="input-txt"/>\n+ </when>\n+ <when value="co">\n+ <expand macro="input-fasta-single"/>\n+ <expand macro="input-txt"/>\n+ </when>\n+ <when value="multi">\n+ <expand macro="input-fasta-multi"/>\n+ <expand macro="input-txt"/>\n+ </when>\n+ </conditional>\n+ </xml>\n <xml name="mode_select">\n <param name="select" type="select" label="Binning mode">\n <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>\n@@ -55,6 +72,12 @@\n <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>\n </param>\n </xml>\n+ <xml name="bam_or_strobealign">\n+ <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">\n+ <option value="bam">BAM</option>\n+ <option value="txt">Strobealign-aemb file(s)</option>\n+ </param>\n+ </xml>\n <xml name="input-fasta-single">\n <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>\n </xml>\n@@ -129,17 +152,27 @@\n <xml name="input-bam-multi">\n <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>\n </xml>\n+ \n+ <xml name="input-txt">\n+ <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>\n+ </xml>\n <token name="@BAM_FILES@"><![CDATA[\n #if $mode.select == \'single\'\n-#set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($input_bam.element_identifier))\n-ln -s \'$input_bam\' \'${identifier}.bam\' &&\n+#set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($mode.input_bam.element_identifier))\n+ln -s \'$mode.input_bam\' \'${identifier}.bam\' &&\n #else\n- #for $e in $input_bam\n+ #for $e in $mode.input_bam\n #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($e.element_identifier))\n ln -s \'$e\' \'${identifier}.bam\' &&\n #end for\n #end if\n ]]></token>\n+ <token name="@STROBEALIGN_FILES@"><![CDATA[\n+#for $e in $mode.align_select.abundance\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($e.element_identifier))\n+ ln -s \'$e\' \'${identifier}.txt\' &&\n+#end for\n+ ]]></token>\n <xml name="ref_select_cannot">\n <param name="select" type="select" label="Reference database">\n <option value="cached">Cached database</option>\n@@ -257,7 +290,6 @@\n <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">\n <option value="fast-naive" selected="true">Fast-Naive</option>\n <option value="prodigal">Prodigal</option>\n- <option value="fraggenescan">Fraggenescan</option>\n </param>\n </xml>\n <xml name="max-node">\n@@ -293,58 +325,153 @@\n </xml>\n <xml name="data_output_single">\n <data name="single_'..b'bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" />\n+ </collection>\n+ <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">\n+ <filter>mode[\'select\']=="multi" and extra_output and "contigs" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" />\n+ </collection>\n+ \n+ <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">\n+ <filter>mode[\'select\']=="co" and extra_output and "coverage" in extra_output</filter>\n+ <filter>mode[\'align_select\']</filter>\n+ <filter>mode[\'align_select\'][\'align_select\']=="txt"</filter>\n+ </data>\n+ <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">\n+ <filter>mode[\'select\']=="co" and extra_output and "coverage" in extra_output</filter>\n+ <filter>mode[\'align_select\']</filter>\n+ <filter>mode[\'align_select\'][\'align_select\']=="txt"</filter>\n+ </data>\n+ \n+ <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">\n+ <filter>mode[\'select\']=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <filter>mode[\'align_select\']</filter>\n+ <filter>mode[\'align_select\'][\'align_select\'] =="txt"</filter>\n+ <discover_datasets pattern="(?P<designation>.*)\\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>\n+ </collection>\n+ <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">\n+ <filter>mode[\'select\']=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <filter>mode[\'align_select\']</filter>\n+ <filter>mode[\'align_select\'][\'align_select\']=="txt"</filter>\n+ <discover_datasets pattern="(?P<designation>.*)\\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>\n+ </collection>\n </xml>\n <xml name="train_output">\n <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />\n@@ -353,31 +480,34 @@\n <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />\n </xml>\n <token name="@HELP_HEADER@"><![CDATA[\n+\n What it does\n ============\n \n SemiBin is a Semi-supervised siamese neural network for metagenomic binning\n-\n-]]></token>\n+ ]]></token>\n <token name="@HELP_INPUT_FASTA@"><![CDATA[\n - Contigs in fasta for 1 or several samples from single or co-assembly\n-]]></token>\n+ ]]></token>\n <token name="@HELP_INPUT_BAM@"><![CDATA[\n - BAM with reads mapping to the contigs\n-]]></token>\n+ ]]></token>\n+ <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[\n+- TXT alignment files that are the output of strobealign-aemb\n+ ]]></token>\n <token name="@HELP_CANNOT@"><![CDATA[\n - Cannot-link constraints\n-]]></token>\n+ ]]></token>\n <token name="@HELP_DATA@"><![CDATA[\n - Training data and split training data for the model\n-]]></token>\n+ ]]></token>\n <token name="@HELP_MODEL@"><![CDATA[\n - Semi-supervised deep learning model\n-]]></token>\n+ ]]></token>\n <token name="@HELP_BINS@"><![CDATA[\n - Reconstructed bins after reclustering\n - Reconstructed bins before reclustering\n-]]></token>\n+ ]]></token>\n <xml name="citations">\n <citations>\n <citation type="doi">10.1038/s41467-022-29843-y</citation>\n'

diff -r 552cfc6ed475 -r 8317c7dc6407 test-data/strobealign_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_1.txt Sun Aug 10 11:37:53 2025 +0000

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diff -r 552cfc6ed475 -r 8317c7dc6407 test-data/strobealign_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_2.txt Sun Aug 10 11:37:53 2025 +0000

diff -r 552cfc6ed475 -r 8317c7dc6407 test-data/strobealign_3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_3.txt Sun Aug 10 11:37:53 2025 +0000

diff -r 552cfc6ed475 -r 8317c7dc6407 test-data/strobealign_4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_4.txt Sun Aug 10 11:37:53 2025 +0000

diff -r 552cfc6ed475 -r 8317c7dc6407 test-data/strobealign_5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_5.txt Sun Aug 10 11:37:53 2025 +0000