# HG changeset patch
# User frogs
# Date 1770211054 0
# Node ID c5fd7b97c2a48a974f49a78448fe0e07c1b5f6b1
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
diff -r 000000000000 -r c5fd7b97c2a4 FROGS_FUNC.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_FUNC.xml Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,90 @@
+
+ Prediction of functional abundances using marker gene sequences
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+ frogs_func_macros.xml
+ picrust2_placeseq_and_copynumber_macros.xml
+ picrust2_functions_macros.xml
+ picrust2_pathways_macros.xml
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+ 10.1093/bioinformatics/btx791
+ 10.1093/bib/bbab318
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diff -r 000000000000 -r c5fd7b97c2a4 frogs_func_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/frogs_func_macros.xml Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,100 @@
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+ 5.1.0
+ 0
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+ frogs
+ picrust2
+ ete3
+ dendropy
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+ --nb-cpus \${GALAXY_SLOTS:-1}
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+ frogs_func_tools['tool_name'] != 'picrust2_pathways'
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+ frogs_func_tools['tool_name'] != 'picrust2_pathways'
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+ frogs_func_tools['tool_name'] != 'picrust2_pathways'
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+ frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber'
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+ frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber'
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+ frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber'
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+ frogs_func_tools['tool_name'] == 'picrust2_functions'
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+ frogs_func_tools['tool_name'] == 'picrust2_functions'
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "EC" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "EC" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "KO" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "KO" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "PFAM" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "PFAM" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "COG" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "COG" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "TIGRFAM" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "TIGRFAM" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "PHENO" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_functions' and "PHENO" in frogs_func_tools['functions']
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+ frogs_func_tools['tool_name'] == 'picrust2_pathways'
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+
diff -r 000000000000 -r c5fd7b97c2a4 picrust2_functions_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picrust2_functions_macros.xml Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,94 @@
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+
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+ frogsfunc_functions.py
+ @CPUS@
+ --input-biom '$input_biom'
+ --input-fasta '$input_fasta'
+ --input-tree '$input_tree'
+ --input-marker-copy '$input_marker_copy'
+ --marker-type $marker.value
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+ #if $marker.value == "16S"
+ --functions ${" ".join(str($functions).split(","))}
+ #end if
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+ #if $marker.value != "16S"
+ --input-function-table $functions.fields.fun
+ #end if
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+ --max-nsti $max_nsti
+ --min-blast-ident $min_blast_ident
+ --min-blast-cov $min_blast_cov
+ --hsp-method '$hsp_method'
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+ --html '$html'
+ --output-excluded '$output_excluded'
+ --output-biom '$output_biom'
+ --output-fasta '$output_fasta'
+ --output-asv-copy-norm '$output_asv_norm'
+ --output-weighted-nsti '$output_weighted_nsti'
+ --prefix-function-abund unstrat_abundance
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\ No newline at end of file
diff -r 000000000000 -r c5fd7b97c2a4 picrust2_pathways_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picrust2_pathways_macros.xml Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,55 @@
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+
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+ frogsfunc_pathways.py
+ @CPUS@
+ --input-tsv '$input_tsv'
+ --map $database.fields.path
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+ #if $normalisation
+ --normalisation
+ #end if
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+ --html $html
+ --output-pathways-abund '$output_pathways_abund'
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\ No newline at end of file
diff -r 000000000000 -r c5fd7b97c2a4 picrust2_placeseq_and_copynumber_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picrust2_placeseq_and_copynumber_macros.xml Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,73 @@
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+
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+ frogsfunc_placeseqs.py
+ @CPUS@
+ --input-fasta '$input_fasta'
+ --input-biom '$input_biom'
+ #if $marker.name != "16S"
+ --ref-dir ${marker.value}
+ --input-marker-table ${marker.fields.traits}
+ #end if
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+ --min-align $min_align
+ --placement-tool '$placement_tool'
+ --hsp-method mp
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+ --output-tree '$output_tree'
+ --excluded '$output_excluded'
+ --output-biom '$output_biom'
+ --output-fasta '$output_fasta'
+ --closests-ref '$output_closests_ref'
+ --output-marker-copy '$output_marker_copy'
+ --html '$html'
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