| Previous changeset 0:1ab06263e083 (2017-03-13) Next changeset 2:ca82f52681af (2017-11-09) |
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Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee |
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modified:
generate_test_data humann2.xml humann2_macros.xml repository_dependencies.xml |
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added:
static/images/731303924-page_DENITRIFICATION-PWY.png test-data/barplot1.png test-data/barplot2.pdf test-data/barplot3.svg test-data/barplot4.png test-data/hmp_pathabund.txt test-data/rename_mapping test-data/rna_dna_norm-dna.txt test-data/rna_dna_norm-rna.txt test-data/strain_profiler-input.txt |
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| diff -r 1ab06263e083 -r 1d6d855c10d8 generate_test_data --- a/generate_test_data Mon Mar 13 12:39:25 2017 -0400 +++ b/generate_test_data Tue Aug 01 07:58:21 2017 -0400 |
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| @@ -48,6 +48,66 @@ --output-basename 'humann2' \ --pathways 'unipathway' +# humann2_associate +humann2_associate \ + --input 'test-data/hmp_pathabund.txt' \ + --focal-metadatum 'STSite' \ + --last-metadatum 'STSite' \ + --focal-type 'categorical' \ + --fdr '0.2' \ + --output 'test-data/associate_output.txt' + +# humann2_barplot +humann2_barplot \ + --input 'test-data/hmp_pathabund.txt' \ + --focal-feature ANAGLYCOLYSIS-PWY \ + --sort none \ + --last-metadatum STSite \ + --focal-metadatum STSite \ + --scaling none \ + --width 5 \ + --dimensions 8 4 \ + --output test-data/barplot1.png + +humann2_barplot \ + --input 'test-data/hmp_pathabund.txt' \ + --focal-feature ANAGLYCOLYSIS-PWY \ + --sort sum \ + --last-metadatum STSite \ + --focal-metadatum STSite \ + --scaling pseudolog \ + --width 5 \ + --dimensions 8 4 \ + --output test-data/barplot2.pdf + +humann2_barplot \ + --input 'test-data/hmp_pathabund.txt' \ + --focal-feature ANAGLYCOLYSIS-PWY \ + --sort metadata \ + --last-metadatum STSite \ + --focal-metadatum STSite \ + --exclude-unclassified \ + --scaling none \ + --as-genera \ + --grid \ + --remove-zeroes \ + --width 5 \ + --dimensions 8 4 \ + --output test-data/barplot3.svg + +humann2_barplot \ + --input 'test-data/hmp_pathabund.txt' \ + --focal-feature ANAGLYCOLYSIS-PWY \ + --top-strata 12 \ + --sort sum \ + --last-metadatum STSite \ + --focal-metadatum STSite \ + --exclude-unclassified \ + --scaling normalize \ + --width 5 \ + --dimensions 8 4 \ + --output test-data/barplot4.eps + # humann2_regroup_table humann2_regroup_table \ --input 'test-data/demo_genefamilies.tsv' \ @@ -111,9 +171,34 @@ # humann2_rename_table humann2_rename_table \ + --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \ + --names 'infogo1000' \ + -o 'test-data/renamed_info1000.tsv' + +humann2_rename_table \ + --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \ + --custom 'test-data/rename_mapping' \ + -o 'test-data/renamed_mapping_info1000.tsv' + +# humann2_rna_dna_norm +humann2_rna_dna_norm \ + --input_dna 'test-data/rna_dna_norm-dna.txt' \ + --input_rna 'test-data/rna_dna_norm-rna.txt' \ + --output_basename 'results1' \ + --method 'laplace' + +humann2_rna_dna_norm \ + --input_dna 'test-data/rna_dna_norm-dna.txt' \ + --input_rna 'test-data/rna_dna_norm-rna.txt' \ + --output_basename 'results2' \ + --method 'witten_bell' \ + --log_transform \ + --log_base '2' + +# humann2_split_stratified_table +humann2_split_stratified_table \ --input 'test-data/demo_genefamilies.tsv' \ - -o 'test-data/renamed_genefamilies.tsv' \ - --names 'metacyc-pwy' + --output 'split_stratified_table' # humann2_split_table mkdir split_table_tmp_dir @@ -122,3 +207,23 @@ -o 'split_table_tmp_dir' cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/' cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/' + +# humann2_strain_profiler +humann2_strain_profiler \ + --input 'test-data/strain_profiler-input.txt' \ + --critical_mean '1' \ + --critical_count '2' \ + --pinterval '1e-10' '1' \ + --critical_samples '2' + +# humann2_unpack_pathways +humann2_unpack_pathways \ + --input-genes 'test-data/demo_genefamilies.tsv' \ + --input-pathways 'test-data/demo_pathabundance.tsv' \ + --output unpack1 + +humann2_unpack_pathways \ + --input-genes 'test-data/demo_genefamilies.tsv' \ + --input-pathways 'test-data/demo_pathabundance.tsv' \ + --remove-taxonomy \ + --output unpack2 |
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| diff -r 1ab06263e083 -r 1d6d855c10d8 humann2.xml --- a/humann2.xml Mon Mar 13 12:39:25 2017 -0400 +++ b/humann2.xml Tue Aug 01 07:58:21 2017 -0400 |
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| b'@@ -12,110 +12,110 @@\n </expand>\n <expand macro="version"/>\n <command detect_errors="exit_code"><
