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Changeset 13:2c8db4bf8834 (2025-11-14)

Previous changeset 12:25a5fa5f86a5 (2024-09-08)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan commit 26cbf16569d13b7ddbbbd99fc49ec15ce312a992

modified:
macros.xml
test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular
test-data/SRS014464-Anterior_nares-abundances.tabular
test-data/SRS014464-Anterior_nares.sam

added:
test-data/SRS014464-Anterior_nares-mapout.tabular

removed:
test-data/SRS014464-Anterior_nares-bowtie2out.tabular
test-data/SRS014464-Anterior_nares-ignore-marker-bowtie2out.tabular
test-data/SRS014464-Anterior_nares-legacy-abundances.tabular
test-data/SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular
test-data/SRS014464-Anterior_nares-two-inputs.sam
test-data/SRS014464-Anterior_nares.biom

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 macros.xml
--- a/macros.xml Sun Sep 08 06:59:54 2024 +0000
+++ b/macros.xml Fri Nov 14 13:47:31 2025 +0000

@@ -1,8 +1,7 @@
-<?xml version="1.0"?>
<macros>
-    <token name="@TOOL_VERSION@">4.1.1</token>
+    <token name="@TOOL_VERSION@">4.2.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">22.05</token>
+    <token name="@PROFILE@">24.0</token>
     
     <token name="@IDX_VERSION@">SGB</token>

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular
--- a/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular Sun Sep 08 06:59:54 2024 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular Fri Nov 14 13:47:31 2025 +0000

b'@@ -1,31 +1,81 @@\n-#custom_db\n-#mpa_v21_CHOCOPhlAnxxx_2\n-#/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\n+#test-db\n+#/home/ubuntu/miniconda3/envs/__metaphlan@4.2.4/bin/metaphlan in --input_type fasta --read_min_len 70 --bt2_ps sensitive --min_mapq_val 5 --db_dir /home/ubuntu/Documents/glxy/git/tools-iuc/tools/metaphlan/test-data/test-db --index test-db -t rel_ab --tax_lev a --stat avg_g --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_98364280-d229-4257-888e-ac290df6e8ca.dat --mapout mapout -s /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_a8ceac4e-3f7c-47e6-bcc3-084f104ca1d8.dat --nproc 1 --offline\n+#17695 reads processed\n #SampleID\tMetaphlan_Analysis\n #clade_name\tNCBI_tax_id\trelative_abundance\tadditional_species\n+UNCLASSIFIED\t-1\t0.0\t\n k__Bacteria\t2\t100.0\t\n-k__Bacteria|p__Proteobacteria\t2|1224\t52.20019\t\n-k__Bacteria|p__Actinobacteria\t2|201174\t34.37371\t\n-k__Bacteria|p__Firmicutes\t2|1239\t13.4261\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria\t2|1224|1236\t52.20019\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria\t2|201174|1760\t34.37371\t\n-k__Bacteria|p__Firmicutes|c__Bacilli\t2|1239|91061\t13.4261\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales\t2|1224|1236|72274\t52.20019\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales\t2|201174|1760|85007\t24.7409\t\n-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales\t2|1239|91061|186826\t13.4261\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales\t2|201174|1760|85009\t9.63281\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae\t2|1224|1236|72274|468\t52.20019\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae\t2|201174|1760|85007|1653\t24.7409\t\n-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae\t2|1239|91061|186826|186828\t13.4261\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae\t2|201174|1760|85009|31957\t9.63281\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella\t2|1224|1236|72274|468|475\t52.20019\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium\t2|201174|1760|85007|1653|1716\t24.7409\t\n-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum\t2|1239|91061|186826|186828|29393\t13.4261\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium\t2|201174|1760|85009|31957|1912216\t9.63281\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata\t2|1224|1236|72274|468|475|477\t22.57968\t\n-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum\t2|201174|1760|85007|1653|1716|37637\t18.75365\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens\t2|1224|1236|72274|468|475|478\t15.88652\t\n-k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi\t2|1224|1236|72274|468|475|60442\t13.73399\t\n-k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobac'..b'Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001660855\t2|201174|1760|85009|31957|1912216|1747|\t2.57775\t\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679005\t2|1224|1236|72274|468|475|478|\t2.55528\t\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_ovis|t__GCA_900453155\t2|1224|1236|72274|468|475|29433|\t2.5544\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264145\t2|1239|91061|186826|186828|29393|29394|\t2.55209\t\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_catarrhalis|t__GCA_000193085\t2|1224|1236|72274|468|475|480|\t2.54518\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263915\t2|1239|91061|186826|186828|29393|29394|\t2.44642\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264015\t2|1239|91061|186826|186828|29393|29394|\t2.42412\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144045\t2|201174|1760|85009|31957|1912216|1747|\t2.16928\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000302515\t2|201174|1760|85009|31957|1912216|1747|\t2.09203\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264135\t2|1239|91061|186826|186828|29393|29394|\t2.07154\t\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis|t__GCA_000177055\t2|976|200643|171549|171552|838|386414|\t1.98596\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263965\t2|1239|91061|186826|186828|29393|29394|\t1.82646\t\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi|t__GCA_900453335\t2|1224|1236|72274|468|475|60442|\t1.72798\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_003384285\t2|201174|1760|85009|31957|1912216|1747|\t1.43296\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000146485\t2|201174|1760|85007|1653|1716|38284|\t1.41285\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudogenitalium|t__GCA_000156615\t2|201174|1760|85007|1653|1716|38303|\t1.3743\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264005\t2|1239|91061|186826|186828|29393|29394|\t1.30558\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144005\t2|201174|1760|85009|31957|1912216|1747|\t1.18889\t\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264085\t2|1239|91061|186826|186828|29393|29394|\t1.13712\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000159115\t2|201174|1760|85007|1653|1716|38284|\t1.03602\t\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001481615\t2|201174|1760|85009|31957|1912216|1747|\t0.55165\t\n'

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-abundances.tabular
--- a/test-data/SRS014464-Anterior_nares-abundances.tabular Sun Sep 08 06:59:54 2024 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances.tabular Fri Nov 14 13:47:31 2025 +0000

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-bowtie2out.tabular
--- a/test-data/SRS014464-Anterior_nares-bowtie2out.tabular Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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No newline at end of file\n'

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-ignore-marker-bowtie2out.tabular
--- a/test-data/SRS014464-Anterior_nares-ignore-marker-bowtie2out.tabular Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-legacy-abundances.tabular
--- a/test-data/SRS014464-Anterior_nares-legacy-abundances.tabular Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-mapout.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-mapout.tabular Fri Nov 14 13:47:31 2025 +0000

b'@@ -0,0 +1,140 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No newline at end of file\n'

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular
--- a/test-data/SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,278 +0,0 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No newline at end of file\n'

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares-two-inputs.sam
--- a/test-data/SRS014464-Anterior_nares-two-inputs.sam Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,377 +0,0 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6\t765\t42\t91M\t*\t0\t0\tCAACGATGGCGCCGCTGTAGAGGGGCAGGCTCACTCGACTACCCCGAAGGCAGAGTTCGGCACCGCGCTTAACCAAGGGGCAACGCCGTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:75G15\tYT:Z:UU\n-HWI-EAS109_102883399:4:86:2354:13206/2\t0\t38303__E2S5B9__HMPREF0305_11721\t628\t42\t100M\t*\t0\t0\tGAGTCGTATCTTCGCTATGGGCAGTTTGTTGATGCAGCCCAAGACTCAGAGAAGATGAGTATTACCGAACTGGTCGATACCGCTATCGAAGAGTCCGATA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:35G64\tYT:Z:UU\n-HWI-EAS109_102883399:3:118:12526:20595/1\t16\t29394__H3NDE2__B8A45_00965\t86\t23\t100M\t*\t0\t0\tAACGTGGGGTGAAAAATCGACCAGCAGGATTACGGACATACAGTTTAGTTTGCTTAGGATCCGCTTTGATTATGTTGACGAATCAATATATTACAGAACA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:29C4A17T8T2C35\tYT:Z:UU\n-HWI-EAS109_102883399:3:35:14701:14421/1\t16\t478__A0A1B8PMT8__A9Z60_01500\t160\t40\t100M\t*\t0\t0\tACTCGTGATAATACTTCACTGGCATTATCAAGTTCTTTGGTTAAAGAAACTGTGGGTGATACCAAAAAAGACTCAGAGATGTTACTGGGACAACTCTCCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:41C2G0C54\tYT:Z:UU\n-HWI-EAS109_102883399:4:51:2231:13778/1\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n-HWI-EAS109_102883399:4:65:18885:8678/1\t16\t37637__V7ZTH7__N579_0112775\t469\t42\t100M\t*\t0\t0\tGATTTTGTTGATGATCCGGATTCTACTCGGATGTTTTCTGAGAACTCCGCCTGCCCAAACGGGCATGCTCTGACGATTGATGAGTATGAACCCCGCTCCT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n-HWI-EAS109_102883399:3:54:17385:9920/2\t0\t29394__H3NE37__B8A45_05170\t63\t42\t100M\t*\t0\t0\tACAGTATTACAACGATCAAGCCTTATTTAAATACGATTGGAACTTTTTCCAATTAAAATTTCAGCCGTATTTACAGGAATTCAAGTTAATTGAAGAAATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n-HWI-EAS109_102883399:4:2:5506:17168/2\t0\t29394__H3NFP2__B8A45_07105\t284\t42\t100M\t*\t0\t0\tGCCTAGCAATTGAGCAAGTTGATGGTAAGTTTATCTTGAAGCTCTATATTTGGGATGGGGCTGAGCATTATTATATGGACATGGATGCTGAGACCGGTGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:10C89\tYT:Z:UU\n-HWI-EAS109_102883399:4:95:2036:2688/2\t16\t478__A0A1B8PJ21__A9Z60_08925\t339\t24\t76M\t*\t0\t0\tCATTTGGGCATCTTCGATCTCTATCACGCCTGAGCGTGAACAAGTGATGGATTTTAGTGAGCCATATTTGAATCAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:0T8G8T57\tYT:Z:UU\n-HWI-EAS109_102883399:4:51:2231:13778/1\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n'

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares.biom
--- a/test-data/SRS014464-Anterior_nares.biom Sun Sep 08 06:59:54 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,1 +0,0 @@
-{"id": "MetaPhlAn_Analysis","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by": "MetaPhlAn","date": "2021-04-09T17:17:44.233735","matrix_element_type": "float","shape": [7, 1],"type": null,"matrix_type": "sparse","data": [[0,0,5.98726],[1,0,18.75365],[2,0,9.63281],[3,0,13.4261],[4,0,13.73399],[5,0,22.57968],[6,0,15.88652]],"rows": [{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Corynebacterium_accolens"]}},{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Corynebacterium_pseudodiphtheriticum"]}},{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Propionibacteriales", "f__Propionibacteriaceae", "g__Cutibacterium", "s__Cutibacterium_acnes"]}},{"id": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Dolosigranulum", "s__Dolosigranulum_pigrum"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_equi"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_lacunata"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_nonliquefaciens"]}}],"columns": [{"id": "Metaphlan_Analysis", "metadata": null}]}
\ No newline at end of file

diff -r 25a5fa5f86a5 -r 2c8db4bf8834 test-data/SRS014464-Anterior_nares.sam
--- a/test-data/SRS014464-Anterior_nares.sam Sun Sep 08 06:59:54 2024 +0000
+++ b/test-data/SRS014464-Anterior_nares.sam Fri Nov 14 13:47:31 2025 +0000

b'@@ -1,4 +1,5 @@\n-@HD\tVN:1.0\tSO:unsorted\n+@CO\tindex:test-db\n+@HD\tVN:1.5\tSO:unsorted\tGO:query\n @SQ\tSN:13076__A0A2I1PE66__CYJ72_10760\tLN:540\n @SQ\tSN:1747__A0A1N4YDI5__CP875_06750\tLN:1164\n @SQ\tSN:1747__A0A1N5AYP4__B1B09_10705\tLN:1476\n@@ -90,146 +91,146 @@\n @SQ\tSN:60442__A0A378QU90__cya_5\tLN:3615\n @SQ\tSN:60442__A0A378QWP5__cya_3\tLN:780\n @SQ\tSN:90240__A0A378QWM4__NCTC12877_00123\tLN:555\n-@PG\tID:bowtie2\tPN:bowtie2\tVN:2.4.2\tCL:"/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/bowtie2-align-s --wrapper basic-0 --quiet --very-sensitive -x ref_db/custom_db -f --passthrough -U -"\n-HWI-EAS109_102883399:3:104:7342:14360/1\t16\t37637__U2I1U8__N579_01580\t335\t42\t100M\t*\t0\t0\tCTTCCCTAATCACGTTACAAGAACCGGCCCGGGCACTATCCCAAGATTCGCGCTCTGGCCGCCTGGTGAGCGAGCGCGACCTGCGCGCCTATGATTGGTT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:16G83\tYT:Z:UU\n-HWI-EAS109_102883399:3:107:9938:7093/1\t0\t90240__A0A378QWM4__NCTC12877_00123\t328\t42\t100M\t*\t0\t0\tTTCATCCAAGGTGGCTACAAAAATGACAACGCATTACAGCTTGTTACCGCCTTTGCCAGTCAAACCAAACTCATTCTTGCTCAAGTTGACATTGCTGATA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n-HWI-EAS109_102883399:3:108:10698:12367/1\t0\t38284__A0A376GA42__HMPREF0276_2319\t125\t42\t93M\t*\t0\t0\tCACGTATCGCCGAACGCGGGCGGGCTGGCATCGTGCCCGACAGCACGGCACCGCTGAACCCGCGACGGGTCTACGATGACAAGATTCGACAAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:93\tYT:Z:UU\n-HWI-EAS109_102883399:3:114:6282:15170/1\t16\t477__A0A1V4GM23__A9Z63_04930\t475\t23\t100M\t*\t0\t0\tCTGGGAAAAATTGAAGGGAAAATTAATGAACAGCAAACCTACATTCAAACCTTGCACGATAAATTACAAAATGAGATTGCAGGTAAAAAAGGTTCAAAAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-24\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:0A15A32A0A49\tYT:Z:UU\n-HWI-EAS109_102883399:3:116:11192:12957/1\t0\t1747__D4HCW6__PAGK_1340\t1061\t42\t100M\t*\t0\t0\tCGATTATGCATCCCCTCATACTCTCCCGATACACCGAGAAACAATGGAACGAGTCACGACACGGCCTCGGTCAGAGTGAAGCCATGGTCATGCTCATGTT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n-HWI-EAS109_102883399:3:118:12526:20595/1\t16\t29394__H3NDE2__B8A45_00965\t86\t23\t100M\t*\t0\t0\tAACGTGGGGTGAAAAATCGACCAGCAGGATTACGGACATACAGTTTAGTTTGCTTAGGATCCGCTTTGATTATGTTGACGAATCAATATATTACAGAACA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:29C4A17T8T2C35\tYT:Z:UU\n-HWI-EAS109_102883399:3:17:12574:2133/1\t16\t478__A0A1B8QSP6__A9Z60_08260\t1172\t24\t91M\t*\t0\t0\tGCCGTCAGCACAAAACCGCGCATAAACACATCAAGCACGCCCGTCAAGACGTCATTCATATTCTATCTCAACACAAAACATTACTGCCCCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:8T42C36T2\tYT:Z:UU\n-HWI-EAS109_102883399:3:21:9846:16342/1\t0\t13076__A0A2I1PE66__CYJ72_10760\t140\t40\t100M\t*\t0\t0\tATCACGATTTAAGTCCTGTCCAATACGCTTACCTAGTGGTGGATGTTATTTATATAAAAGTAAGAGAAAATCATAAGGTTGTATCGAAAGCATGCCATAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:85C5G8\tYT:Z:UU\n-HWI-EAS109_102883399:3:24:9356:13561/1\t0\t478__A0A1B8PJN3__A9Z65_07575\t973\t42\t100M\t*\t0\t0\tCTTATGATGATACAGGACTTAGCTGTCATACATAATAAAATATTAATCGCAATTATTGAAAAAAGCAGTCCACAAAACTGGCAAAAACTCATTGAACAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:76G23\tYT:Z:UU\n-HWI-EAS109_102883399:3:31:18846:14786/1\t16\t478__A0A1B8PLP8__A9Z60_06460\t1755\t42\t89M\t*\t0\t0\tGGCAACCGCTTATGCCACTTTTGCCAACGGTGGTCATCGGATTCAGCCTTATATCATTGAACGCATTTATAATTTTCATAATGAAACCA\tIIIIIIIII'..b'ATGGTGTTCCGGGCCGTGCAGGTGCTGACGGTGTGAACGGCGCTGATGGTCGGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-36\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:14T17G15T28T3C2C4\tYT:Z:UU\n+HWI-EAS109_102883399:3:69:13778:8249/2__1.17679\t0\t1747__A0A1N5AYP4__B1B09_10705\t368\t42\t79M\t*\t0\t0\tTCCTCATCGCGGGTGGTATGAGCTACGGCCCGCAGACCAAGGCTTTTAAGAGGGGAGTCGACCTTGTTGTCGCCACCCC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:79\tYT:Z:UU\n+HWI-EAS109_102883399:4:43:7696:5439/2__1.18586\t0\t38284__C0WL80__HMPREF0276_2216\t765\t42\t91M\t*\t0\t0\tCAACGATGGCGCCGCTGTAGAGGGGCAGGCTCACTCGACTACCCCGAAGGCAGAGTTCGGCACCGCGCTTAACCAAGGGGCAACGCCGTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:75G15\tYT:Z:UU\n+HWI-EAS109_102883399:4:86:2354:13206/2__1.18981\t0\t38303__E2S5B9__HMPREF0305_11721\t628\t42\t100M\t*\t0\t0\tGAGTCGTATCTTCGCTATGGGCAGTTTGTTGATGCAGCCCAAGACTCAGAGAAGATGAGTATTACCGAACTGGTCGATACCGCTATCGAAGAGTCCGATA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:35G64\tYT:Z:UU\n+HWI-EAS109_102883399:3:118:12526:20595/1__1.19173\t16\t29394__H3NDE2__B8A45_00965\t86\t23\t100M\t*\t0\t0\tAACGTGGGGTGAAAAATCGACCAGCAGGATTACGGACATACAGTTTAGTTTGCTTAGGATCCGCTTTGATTATGTTGACGAATCAATATATTACAGAACA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:29C4A17T8T2C35\tYT:Z:UU\n+HWI-EAS109_102883399:3:35:14701:14421/1__1.19246\t16\t478__A0A1B8PMT8__A9Z60_01500\t160\t40\t100M\t*\t0\t0\tACTCGTGATAATACTTCACTGGCATTATCAAGTTCTTTGGTTAAAGAAACTGTGGGTGATACCAAAAAAGACTCAGAGATGTTACTGGGACAACTCTCCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:41C2G0C54\tYT:Z:UU\n+HWI-EAS109_102883399:4:51:2231:13778/1__1.19508\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n+HWI-EAS109_102883399:4:65:18885:8678/1__1.19529\t16\t37637__V7ZTH7__N579_0112775\t469\t42\t100M\t*\t0\t0\tGATTTTGTTGATGATCCGGATTCTACTCGGATGTTTTCTGAGAACTCCGCCTGCCCAAACGGGCATGCTCTGACGATTGATGAGTATGAACCCCGCTCCT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+HWI-EAS109_102883399:3:54:17385:9920/2__1.19752\t0\t29394__H3NE37__B8A45_05170\t63\t42\t100M\t*\t0\t0\tACAGTATTACAACGATCAAGCCTTATTTAAATACGATTGGAACTTTTTCCAATTAAAATTTCAGCCGTATTTACAGGAATTCAAGTTAATTGAAGAAATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+HWI-EAS109_102883399:4:2:5506:17168/2__1.19961\t0\t29394__H3NFP2__B8A45_07105\t284\t42\t100M\t*\t0\t0\tGCCTAGCAATTGAGCAAGTTGATGGTAAGTTTATCTTGAAGCTCTATATTTGGGATGGGGCTGAGCATTATTATATGGACATGGATGCTGAGACCGGTGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:10C89\tYT:Z:UU\n+HWI-EAS109_102883399:4:95:2036:2688/2__1.20089\t16\t478__A0A1B8PJ21__A9Z60_08925\t339\t24\t76M\t*\t0\t0\tCATTTGGGCATCTTCGATCTCTATCACGCCTGAGCGTGAACAAGTGATGGATTTTAGTGAGCCATATTTGAATCAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:0T8G8T57\tYT:Z:UU\n+HWI-EAS109_102883399:4:51:2231:13778/1__1.20252\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n'