# HG changeset patch # User bebatut # Date 1487698177 18000 # Node ID 83f06bee818c505c7529bac6240eb27dbe93ea84 # Parent 99fe591b59fb67adfcb8e8ae414ad9828d087ddf planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty diff -r 99fe591b59fb -r 83f06bee818c extract_markers.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_markers.xml Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,50 @@ + + + output for Krona + + + metaphlan2_macros.xml + + + + + + extract_markers.py -v + + + + + + + + + + + + + + + + + + + + + `_. + +This tool formats MetaPhlAn2 output to be ready for Krona. + + ]]> + + + diff -r 99fe591b59fb -r 83f06bee818c generate_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,49 @@ +#/usr/bin/env bash + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.png \ + -m 'average' \ + -d 'braycurtis' \ + -f 'correlation' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'jet' + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.pdf \ + -m 'ward' \ + -d 'euclidean' \ + -f 'euclidean' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'pink' + +metaphlan_hclust_heatmap.py \ + --in test-data/merged_community_profile.tabular \ + --out test-data/heatmap.svg \ + -m 'complete' \ + -d 'hamming' \ + -f 'matching' \ + --minv '0' \ + --tax_lev 'a' \ + --sdend_h '0.1' \ + --fdend_w '0.1' \ + --cm_h '0.03' \ + --font_size '7' \ + --clust_line_w '1' \ + --perc '90' \ + -c 'pink' \ No newline at end of file diff -r 99fe591b59fb -r 83f06bee818c merge_metaphlan_tables.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_metaphlan_tables.xml Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,55 @@ + + + MetaPhlAn2 files + + + metaphlan2_macros.xml + + + + + + merge_metaphlan_tables.py -v + + + '$output' +]]> + + + + + + + + + + + + + + + + + + + + + + + `_. + +This tool performs a table join on one or more metaphlan output files + + ]]> + + + diff -r 99fe591b59fb -r 83f06bee818c metaphlan2.xml --- a/metaphlan2.xml Thu Jun 16 06:07:23 2016 -0400 +++ b/metaphlan2.xml Tue Feb 21 12:29:37 2017 -0500 @@ -1,4 +1,4 @@ - + to profile the composition of microbial communities @@ -6,7 +6,10 @@ metaphlan2_macros.xml - + + bowtie2 + + @@ -24,87 +27,85 @@ #if $db.db_selector == "history" mkdir ref_db && - bowtie2-build $db.db_sequences ref_db/ref_db + bowtie2-build '$db.bowtie2db' 'ref_db/ref_db' && - python $__tool_directory__/transform_json_to_pkl.py - --json_input $db_metadata - --pkl_output ref_db/metadata.pkl + python '$__tool_directory__/transform_json_to_pkl.py' + --json_input '$db.mpa_pkl' + --pkl_output 'ref_db/metadata.pkl' && #end if metaphlan2.py - $input_file - -o $output_file - --input_type ${input_file.datatype.file_ext} + '$input_file' + -o '$output_file' + --input_type '${input_file.datatype.file_ext}' --bowtie2_exe `which bowtie2` #if $db.db_selector == "cached" #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data]) #set $db_choice = $db.cached_db.value - --bowtie2db $table[$db_choice] + --bowtie2db '$table[$db_choice]' --mpa_pkl $table[$db_choice]".pkl" #else - --bowtie2db ref_db/ref_db - --mpa_pkl ref_db/metadata.pkl + --bowtie2db 'ref_db/ref_db' + --mpa_pkl 'ref_db/metadata.pkl' #end if --no_map - -t $analysis_type.analysis_type_select - #if $analysis_type.analysis_type_select == "rel_ab" - --tax_lev $analysis_type.taxonomic_level + -t '$analysis_type.analysis_type_select' + #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats" + --tax_lev '$analysis_type.taxonomic_level' #else if $analysis_type.analysis_type_select == "marker_ab_table" - --nreads $analysis_type.nreads + --nreads '$analysis_type.nreads' #else if $analysis_type.analysis_type_select == "marker_pres_table" - --pres_th $analysis_type.pres_th + --pres_th '$analysis_type.pres_th' #end if - --min_cu_len $min_cu_len - --min_alignment_len $min_alignment_len + --min_cu_len '$min_cu_len' + --min_alignment_len '$min_alignment_len' $ignore_viruses $ignore_eukaryotes $ignore_bacteria $ignore_archaea - --stat_q $stat_q - -s $sam_output_file + --stat_q '$stat_q' + -s '$sam_output_file' + --biom '$biom_output_file' ]]> - - - + - - + + - - + + - - + @@ -115,46 +116,51 @@ - + + + + + + + + + + + + - - + - - - + - - - - - - - - - - - - - + + + + + + + + + + - - + + @@ -164,6 +170,8 @@ + + @@ -207,7 +215,5 @@ ]]> - - 10.1038/nmeth.3589 - + diff -r 99fe591b59fb -r 83f06bee818c metaphlan2_macros.xml --- a/metaphlan2_macros.xml Thu Jun 16 06:07:23 2016 -0400 +++ b/metaphlan2_macros.xml Tue Feb 21 12:29:37 2017 -0500 @@ -1,10 +1,10 @@ + 2.6.0 - bowtie2 - numpy - metaphlan2 + metaphlan2 + @@ -20,4 +20,9 @@ description="" /> + + + 10.1038/nmeth.3589 + + diff -r 99fe591b59fb -r 83f06bee818c metaphlan2krona.xml --- a/metaphlan2krona.xml Thu Jun 16 06:07:23 2016 -0400 +++ b/metaphlan2krona.xml Tue Feb 21 12:29:37 2017 -0500 @@ -1,4 +1,4 @@ - + output for Krona @@ -9,22 +9,18 @@ - - - + metaphlan2krona.py -v - + @@ -33,7 +29,7 @@ - + @@ -48,7 +44,5 @@ ]]> - - 10.1038/nmeth.3589 - + diff -r 99fe591b59fb -r 83f06bee818c metaphlan_hclust_heatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan_hclust_heatmap.xml Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,276 @@ + + + with hierarchical clustering of both samples +and microbial clades for MetaPhlAn2 + + + metaphlan2_macros.xml + + + + + + metaphlan_hclust_heatmap.py -v + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + output_format == "pdf" + + + output_format == "png" + + + output_format == "svg" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_. + +This tool generates heatmaps with hierarchical clustering of both samples +and microbial clades. The script can also subsample the number of clades to +display based on the their nth percentile abundance value in each sample + + ]]> + + + diff -r 99fe591b59fb -r 83f06bee818c repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,4 @@ + + + + diff -r 99fe591b59fb -r 83f06bee818c test-data/heatmap.pdf Binary file test-data/heatmap.pdf has changed diff -r 99fe591b59fb -r 83f06bee818c test-data/heatmap.png Binary file test-data/heatmap.png has changed diff -r 99fe591b59fb -r 83f06bee818c test-data/heatmap.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.svg Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,1291 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 99fe591b59fb -r 83f06bee818c test-data/merged_community_profile.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_community_profile.tabular Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,11 @@ +ID community_profile community_profile +k__Bacteria 100.0 100.0 +k__Bacteria|p__Bacteroidetes 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 100.0 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris 68.05418 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris|t__Bacteroides_stercoris_unclassified 68.05418 68.05418 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron 31.94582 31.94582 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified 31.94582 31.94582 diff -r 99fe591b59fb -r 83f06bee818c tool-data/metaphlan2_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan2_database.loc.sample Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file diff -r 99fe591b59fb -r 83f06bee818c tool-data/metaphlan2_db.loc.sample --- a/tool-data/metaphlan2_db.loc.sample Thu Jun 16 06:07:23 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# Bowtie2 db have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/src/5424bb911dfc/db_v20/?at=default (whole directory) -# -#Since MetaPhlAn comes bundled with 1 Bowtie2 database, you can use it -#by downloading it as explained above and uncommenting the following lines. -#mpa_v20_m200 Defaut database with clade-specific marker genes $METAPHLAN2_DIR/db_v20/mpa_v20_m200 diff -r 99fe591b59fb -r 83f06bee818c tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Jun 16 06:07:23 2016 -0400 +++ b/tool_data_table_conf.xml.sample Tue Feb 21 12:29:37 2017 -0500 @@ -1,6 +1,6 @@ - +
value, name, path - +
diff -r 99fe591b59fb -r 83f06bee818c tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 16 06:07:23 2016 -0400 +++ b/tool_dependencies.xml Tue Feb 21 12:29:37 2017 -0500 @@ -1,7 +1,7 @@ - + diff -r 99fe591b59fb -r 83f06bee818c transform_json_to_pkl.py --- a/transform_json_to_pkl.py Thu Jun 16 06:07:23 2016 -0400 +++ b/transform_json_to_pkl.py Tue Feb 21 12:29:37 2017 -0500 @@ -1,10 +1,11 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -import cPickle as pickle +import argparse import bz2 +import cPickle as pickle import json -import argparse + def transform_json_to_pkl(args): with open(args.json_input, 'r') as json_file: @@ -12,17 +13,18 @@ metadata = json.loads(json_str) for marker in metadata["markers"]: - metadata["markers"][marker]["ext"] = set(metadata["markers"][marker]["ext"]) + a_set = set(metadata["markers"][marker]["ext"]) + metadata["markers"][marker]["ext"] = a_set pkl_output = bz2.BZ2File(args.pkl_output, 'w') pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) pkl_output.close() + if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('--json_input', required=True) parser.add_argument('--pkl_output', required=True) - args = parser.parse_args() transform_json_to_pkl(args)