# HG changeset patch
# User iuc
# Date 1723408409 0
# Node ID deff72a7700d9c638f57035841384b1c68dccd5f
# Parent  3b73897fd779693fbe8b9d21510b0215b5a7f95c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 671a5fc6d4c02bd3eb830c1886a31ecffd134ceb

diff -r 3b73897fd779 -r deff72a7700d customize_metaphlan_database.xml
--- a/customize_metaphlan_database.xml	Thu Apr 20 11:24:22 2023 +0000
+++ b/customize_metaphlan_database.xml	Sun Aug 11 20:33:29 2024 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="requirements">
-        <requirement type="package" version="1.3">seqtk</requirement>
+        <requirement type="package" version="1.4">seqtk</requirement>
     </expand>
     <version_command>metaphlan -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 3b73897fd779 -r deff72a7700d macros.xml
--- a/macros.xml	Thu Apr 20 11:24:22 2023 +0000
+++ b/macros.xml	Sun Aug 11 20:33:29 2024 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">4.0.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">4.1.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <!-- Metaphlan DB compatible with this version of Metaphlan
     v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> 
@@ -23,4 +23,9 @@
             <citation type="doi">10.7554/eLife.65088</citation>
         </citations>
     </xml>
+
+    <xml name="subsample_common">
+        <param argument="--mapping_subsampling" type="boolean" truevalue="--mapping_subsampling" falsevalue="" label="Subsampling on the mapping results" help="instead of on the reads"/>
+        <param argument="--subsampling_seed" type="integer" optional="true" label="Subsampling seed" help="No value: random"/>
+    </xml>
 </macros>
diff -r 3b73897fd779 -r deff72a7700d test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular	Sun Aug 11 20:33:29 2024 +0000
@@ -0,0 +1,31 @@
+#custom_db
+#mpa_v21_CHOCOPhlAnxxx_2
+#/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/metaphlan in --input_type fasta --read_min_len 70 --bowtie2db ref_db/ --index custom_db --bt2_ps very-sensitive --min_mapq_val 5 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmptu3575j7/files/000/dataset_19.dat --bowtie2out bowtie2out -s /tmp/tmptu3575j7/files/000/dataset_21.dat --biom /tmp/tmptu3575j7/files/000/dataset_22.dat --nproc 1
+#SampleID	Metaphlan_Analysis
+#clade_name	NCBI_tax_id	relative_abundance	additional_species
+k__Bacteria	2	100.0	
+k__Bacteria|p__Proteobacteria	2|1224	52.20019	
+k__Bacteria|p__Actinobacteria	2|201174	34.37371	
+k__Bacteria|p__Firmicutes	2|1239	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	2|1224|1236	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria	2|201174|1760	34.37371	
+k__Bacteria|p__Firmicutes|c__Bacilli	2|1239|91061	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2|1224|1236|72274	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales	2|201174|1760|85007	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2|1239|91061|186826	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales	2|201174|1760|85009	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	2|1224|1236|72274|468	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae	2|201174|1760|85007|1653	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae	2|1239|91061|186826|186828	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae	2|201174|1760|85009|31957	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella	2|1224|1236|72274|468|475	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium	2|201174|1760|85007|1653|1716	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum	2|1239|91061|186826|186828|29393	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium	2|201174|1760|85009|31957|1912216	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata	2|1224|1236|72274|468|475|477	22.57968	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum	2|201174|1760|85007|1653|1716|37637	18.75365	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens	2|1224|1236|72274|468|475|478	15.88652	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi	2|1224|1236|72274|468|475|60442	13.73399	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum	2|1239|91061|186826|186828|29393|29394	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes	2|201174|1760|85009|31957|1912216|1747	9.63281	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens	2|201174|1760|85007|1653|1716|38284	5.98726	
diff -r 3b73897fd779 -r deff72a7700d test-data/SRS014464-Anterior_nares.fastq.gz
Binary file test-data/SRS014464-Anterior_nares.fastq.gz has changed
diff -r 3b73897fd779 -r deff72a7700d test-data/test_database_versioned.loc
--- a/test-data/test_database_versioned.loc	Thu Apr 20 11:24:22 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# Tab separated with 5 columns:
-# - value (Galaxy records this in the Galaxy DB)
-# - name (Galaxy shows this in the UI)
-# - value (Galaxy records this in the Galaxy DB)
-# - path (folder name containing the Kraken DB)
-# - db version (whether it is SGB of Metaphlan v4 or not)
-test-db-20210409	"Test Database"	test-db	${__HERE__}/test-db	SGB
diff -r 3b73897fd779 -r deff72a7700d test-data/test_database_versioned.loc.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database_versioned.loc.test	Sun Aug 11 20:33:29 2024 +0000
@@ -0,0 +1,11 @@
+# Tab separated with 5 columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - dbkey
+# - path (folder name containing the Kraken DB)
+# - db version (whether it is SGB of Metaphlan v4 or not)
+test-db-20210409	"Test Database"	test-db	${__HERE__}/test-db	SGB
+# the TOY DB should be called in tests with the hidden test parameter enables this will make Metaphlan
+# download the data to the JWD
+mpa_vJan21_TOY_CHOCOPhlAnSGB	mpa_vJan21_TOY_CHOCOPhlAnSGB	mpa_vJan21_TOY_CHOCOPhlAnSGB_202103	./	SGB
+# mpa_vJun23_CHOCOPhlAnSGB_202403	mpa_vJun23_CHOCOPhlAnSGB_202403	mpa_vJun23_CHOCOPhlAnSGB_202403	${__HERE__}/mpa_vJun23_CHOCOPhlAnSGB_202403/	SGB
diff -r 3b73897fd779 -r deff72a7700d tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Thu Apr 20 11:24:22 2023 +0000
+++ b/tool_data_table_conf.xml.test	Sun Aug 11 20:33:29 2024 +0000
@@ -2,6 +2,6 @@
 <tables>
     <table name="metaphlan_database_versioned" comment_char="#">
         <columns>value, name, dbkey, path, db_version</columns>
-        <file path="${__HERE__}/test-data/test_database_versioned.loc"/>
+        <file path="${__HERE__}/test-data/test_database_versioned.loc.test"/>
     </table>
 </tables>