| Previous changeset 11:0270541aaf46 (2023-04-20) Next changeset 13:327d9f4cc95f (2024-04-30) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 70ba929dd55348ee43753e6ae29bd45c5cdf5471 |
|
modified:
macros.xml merge_metaphlan_tables.xml |
|
added:
test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular |
| b |
| diff -r 0270541aaf46 -r 7f5d7b0e9884 macros.xml --- a/macros.xml Thu Apr 20 11:26:31 2023 +0000 +++ b/macros.xml Sat Feb 10 23:56:53 2024 +0000 |
| b |
| @@ -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="@VERSION_SUFFIX@">2</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 --> |
| b |
| diff -r 0270541aaf46 -r 7f5d7b0e9884 merge_metaphlan_tables.xml --- a/merge_metaphlan_tables.xml Thu Apr 20 11:26:31 2023 +0000 +++ b/merge_metaphlan_tables.xml Sat Feb 10 23:56:53 2024 +0000 |
| [ |
| @@ -7,9 +7,13 @@ <expand macro="requirements"/> <version_command>metaphlan -v</version_command> <command detect_errors="aggressive"><![CDATA[ -merge_metaphlan_tables.py - #for $element in $inputs - '$element' + #for $input in $inputs + ln -s '$input' '${input.element_identifier}' && + #end for + + merge_metaphlan_tables.py + #for $input in $inputs + '${input.element_identifier}' #end for > '$output' ]]> @@ -22,11 +26,12 @@ </outputs> <tests> <test expect_num_outputs="1"> - <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/> + <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular"/> <output name="output" ftype="tabular"> <assert_contents> <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> - <has_text text="dataset_"/> + <has_text text="SRS014464-Anterior_nares-abundances"/> + <has_text text="SRS014464-Anterior_nares-abundances-samefiledifferentname"/> <has_text text="clade_name"/> <has_line_matching expression="#.*"/> </assert_contents> |
| b |
| diff -r 0270541aaf46 -r 7f5d7b0e9884 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 Sat Feb 10 23:56:53 2024 +0000 |
| b |
| @@ -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 |