# HG changeset patch
# User bgruening
# Date 1665783123 0
# Node ID dba4c0409de12530d848cafd3709fc889fb0b4ae
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
diff -r 000000000000 -r dba4c0409de1 generate_cannot_links.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_cannot_links.xml Fri Oct 14 21:32:03 2022 +0000
@@ -0,0 +1,138 @@
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+ macros.xml
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diff -r 000000000000 -r dba4c0409de1 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 14 21:32:03 2022 +0000
@@ -0,0 +1,351 @@
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+ 1.1.1
+ 0
+ 21.01
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+ semibin
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+ semibin
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+ SemiBin -v
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+ 'contigs.fasta' &&
+#else
+ln -s '$input_fasta' 'contigs.fasta' &&
+#end if
+ ]]>
+ 'contigs.fasta' &&
+ #else
+ln -s '$mode.input_fasta' 'contigs.fasta' &&
+ #end if
+#else
+ #if $mode.multi_fasta.select == 'concatenated'
+ #if $mode.multi_fasta.input_fasta.ext.endswith(".gz")
+gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' &&
+ #else
+ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' &&
+ #end if
+#set $separator = $mode.multi_fasta.separator
+ #else
+ #for $e in $mode.multi_fasta.input_fasta
+ #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+ #if $e.ext.endswith(".gz")
+gunzip -c '$e' > '${identifier}.fasta' &&
+ #else
+ln -s '$e' '${identifier}.fasta' &&
+ #end if
+ #end for
+#set $separator = ':'
+SemiBin concatenate_fasta
+ --input-fasta *.fasta
+ --output 'output'
+ --separator '$separator'
+ -m $mode.multi_fasta.min_len
+&&
+ln -s 'output/concatenated.fa' 'contigs.fasta' &&
+ #end if
+#end if
+ ]]>
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+ mode["select"]=="single" or mode["select"]=="co"
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+ mode["select"]=="single" or mode["select"]=="co"
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+ mode["select"]=="multi"
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+ mode["select"]=="multi"
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+ mode["select"]=="single" and extra_output and "coverage" in extra_output
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+ mode["select"]=="single" and extra_output and "coverage" in extra_output
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+ mode["select"]=="co" and extra_output and "coverage" in extra_output
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+ mode["select"]=="co" and extra_output and "coverage" in extra_output
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+ mode["select"]=="multi" and extra_output and "coverage" in extra_output
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+ mode["select"]=="multi" and extra_output and "coverage" in extra_output
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+ mode["select"]=="multi" and extra_output and "coverage" in extra_output
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+ mode["select"]=="multi" and extra_output and "coverage" in extra_output
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+ mode["select"]=="multi" and extra_output and "contigs" in extra_output
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+ 10.1038/s41467-022-29843-y
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