| Previous changeset 0:dd4b5b9daf6b (2017-03-13) Next changeset 2:059d752e3a1a (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_macros.xml humann2_rename_table.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 dd4b5b9daf6b -r b6d4c448782f generate_test_data --- a/generate_test_data Mon Mar 13 12:37:08 2017 -0400 +++ b/generate_test_data Tue Aug 01 07:55:21 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 dd4b5b9daf6b -r b6d4c448782f humann2_macros.xml --- a/humann2_macros.xml Mon Mar 13 12:37:08 2017 -0400 +++ b/humann2_macros.xml Tue Aug 01 07:55:21 2017 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">0.9.9</token> + <token name="@WRAPPER_VERSION@">0.11.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">humann2</requirement> |
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| diff -r dd4b5b9daf6b -r b6d4c448782f humann2_rename_table.xml --- a/humann2_rename_table.xml Mon Mar 13 12:37:08 2017 -0400 +++ b/humann2_rename_table.xml Tue Aug 01 07:55:21 2017 -0400 |
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| @@ -6,47 +6,74 @@ <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ - humann2_rename_table - --input '$input' - -o '$output_table' - --names '$names' - $simplify - #if $custom - --custom '$custom' - #end if +humann2_rename_table + --input '$input' + -o '$output_table' + #if $renaming.type == 'standard' + --names '$renaming.names' + #else + --custom '$renaming.custom' + #end if + $simplify ]]></command> <inputs> <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> - <param argument="--names" type="select" label="Table features that can be renamed"> - <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> - <option value="metacyc-pwy">MetaCyc pathways</option> - <option value="infogo1000">InfoGO1000</option> - <option value="uniref90">UniRef90</option> - <option value="kegg-module">KEGG Module</option> - <option value="ec">Enzyme commision (EC)</option> - <option value="go">Gene Ontology (GO)</option> - <option value="pfam">PFAM</option> - <option value="eggnog">eggNOG</option> - <option value="uniref50">UniRef50</option> - <option value="kegg-pathway">KEGG Pathway</option> - <option value="kegg-orthology">KEGG Orthology</option> - </param> - <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/> - <param argument="--custom" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value" optional="true"/> + <conditional name="renaming"> + <param name="type" type="select" label="Type of renaming"> + <option value="standard">Standard renaming</option> + <option value="custom">Custom renaming</option> + </param> + <when value="standard"> + <param argument="--names" type="select" label="Table features that can be renamed"> + <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> + <option value="metacyc-pwy">MetaCyc pathways</option> + <option value="infogo1000">InfoGO1000</option> + <option value="kegg-module">KEGG Module</option> + <option value="ec">Enzyme commision (EC)</option> + <option value="go">Gene Ontology (GO)</option> + <option value="pfam">PFAM</option> + <option value="eggnog">eggNOG</option> + <option value="uniref50">UniRef50</option> + <!--<option value="uniref90">UniRef90</option>--> + <option value="kegg-pathway">KEGG Pathway</option> + <option value="kegg-orthology">KEGG Orthology</option> + </param> + </when> + <when value="custom"> + <param argument="--custom" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value"/> + </when> + </conditional> + <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/> </inputs> <outputs> <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" /> </outputs> <tests> <test> - <param name="input" value="demo_genefamilies.tsv"/> - <param name="names" value="uniref90" /> + <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/> + <conditional name="renaming"> + <param name="type" value="standard"/> + <param name="names" value="infogo1000" /> + </conditional> <param name="simplify" value=""/> <output name="output_table"> <assert_contents> - <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" /> - <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" /> - <has_text text="UniRef90_C3RF26: HRDC domain protein" /> + <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" /> + <has_text text="GO:0000287: [MF] magnesium ion binding" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/> + <conditional name="renaming"> + <param name="type" value="custom"/> + <param name="custom" value="rename_mapping" /> + </conditional> + <param name="simplify" value=""/> + <output name="output_table"> + <assert_contents> + <has_text text="GO:0000015: GO1" /> + <has_text text="GO:0000107: NO_NAME" /> </assert_contents> </output> </test> |
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| diff -r dd4b5b9daf6b -r b6d4c448782f repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 13 12:37:08 2017 -0400 +++ b/repository_dependencies.xml Tue Aug 01 07:55:21 2017 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories description="This requires the HUMAnN2 data manager definition to install all required databases."> <repository changeset_revision="9c4ad82be5bd" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="1316375a8cbb" name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="854d9862a9f1" name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r dd4b5b9daf6b -r b6d4c448782f static/images/731303924-page_DENITRIFICATION-PWY.png |
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| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/barplot2.pdf |
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| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/barplot3.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barplot3.svg Tue Aug 01 07:55:21 2017 -0400 |
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| b |
| b'@@ -0,0 +1,500 @@\n+FEATURE \\ SAMPLE\tSRS011084\tSRS011086\tSRS011090\tSRS011098\tSRS011111\tSRS011115\tSRS011126\tSRS011132\tSRS011134\tSRS011140\tSRS011144\tSRS011152\tSRS011239\tSRS011243\tSRS011247\tSRS011255\tSRS011263\tSRS011269\tSRS011302\tSRS011306\tSRS011310\tSRS011343\tSRS011355\tSRS011397\tSRS011405\tSRS011584\tSRS012273\tSRS012279\tSRS012281\tSRS012285\tSRS012291\tSRS012294\tSRS012663\tSRS012902\tSRS013155\tSRS013158\tSRS013164\tSRS013170\tSRS013215\tSRS013234\tSRS013239\tSRS013252\tSRS013269\tSRS013476\tSRS013502\tSRS013506\tSRS013521\tSRS013533\tSRS013542\tSRS013687\tSRS013705\tSRS013711\tSRS013723\tSRS013800\tSRS013818\tSRS013825\tSRS013836\tSRS013876\tSRS013879\tSRS013881\tSRS013945\tSRS013949\tSRS013951\tSRS013956\tSRS014124\tSRS014126\tSRS014235\tSRS014271\tSRS014287\tSRS014313\tSRS014343\tSRS014459\tSRS014464\tSRS014470\tSRS014472\tSRS014476\tSRS014494\tSRS014573\tSRS014575\tSRS014578\tSRS014613\tSRS014629\tSRS014682\tSRS014683\tSRS014684\tSRS014686\tSRS014690\tSRS014888\tSRS014890\tSRS014894\tSRS014901\tSRS014923\tSRS014979\tSRS015038\tSRS015040\tSRS015044\tSRS015051\tSRS015054\tSRS015133\tSRS015154\tSRS015158\tSRS015168\tSRS015174\tSRS015190\tSRS015209\tSRS015215\tSRS015217\tSRS015225\tSRS015264\tSRS015269\tSRS015272\tSRS015274\tSRS015278\tSRS015369\tSRS015374\tSRS015378\tSRS015395\tSRS015425\tSRS015430\tSRS015431\tSRS015434\tSRS015436\tSRS015440\tSRS015540\tSRS015574\tSRS015578\tSRS015640\tSRS015644\tSRS015646\tSRS015650\tSRS015663\tSRS015745\tSRS015752\tSRS015755\tSRS015762\tSRS015782\tSRS015890\tSRS015893\tSRS015895\tSRS015899\tSRS015937\tSRS015941\tSRS015960\tSRS015985\tSRS015989\tSRS015996\tSRS016002\tSRS016018\tSRS016033\tSRS016037\tSRS016039\tSRS016043\tSRS016056\tSRS016086\tSRS016092\tSRS016095\tSRS016111\tSRS016188\tSRS016191\tSRS016196\tSRS016200\tSRS016203\tSRS016225\tSRS016267\tSRS016292\tSRS016297\tSRS016319\tSRS016331\tSRS016335\tSRS016342\tSRS016349\tSRS016360\tSRS016434\tSRS016495\tSRS016501\tSRS016503\tSRS016513\tSRS016516\tSRS016541\tSRS016569\tSRS016575\tSRS016581\tSRS016600\tSRS016740\tSRS016746\tSRS016752\tSRS016753\tSRS016954\tSRS016989\tSRS017007\tSRS017013\tSRS017025\tSRS017044\tSRS017076\tSRS017080\tSRS017103\tSRS017120\tSRS017127\tSRS017139\tSRS017156\tSRS017191\tSRS017209\tSRS017215\tSRS017227\tSRS017244\tSRS017247\tSRS017304\tSRS017307\tSRS017433\tSRS017439\tSRS017441\tSRS017445\tSRS017451\tSRS017497\tSRS017520\tSRS017521\tSRS017687\tSRS017697\tSRS017700\tSRS017701\tSRS017713\tSRS017808\tSRS017810\tSRS017814\tSRS017820\tSRS017821\tSRS018133\tSRS018145\tSRS018149\tSRS018157\tSRS018300\tSRS018312\tSRS018313\tSRS018329\tSRS018337\tSRS018351\tSRS018357\tSRS018359\tSRS018369\tSRS018394\tSRS018427\tSRS018439\tSRS018463\tSRS018569\tSRS018573\tSRS018575\tSRS018585\tSRS018591\tSRS018656\tSRS018661\tSRS018665\tSRS018671\tSRS018739\tSRS018769\tSRS018774\tSRS018784\tSRS018791\tSRS018817\tSRS019215\tSRS019219\tSRS019221\tSRS019225\tSRS019245\tSRS019267\tSRS019327\tSRS019329\tSRS019333\tSRS019339\tSRS019379\tSRS019381\tSRS019386\tSRS019387\tSRS019389\tSRS019391\tSRS019397\tSRS019587\tSRS019591\tSRS019597\tSRS019600\tSRS019601\tSRS019607\tSRS019968\tSRS019974\tSRS019976\tSRS019980\tSRS019986\tSRS019989\tSRS020220\tSRS020222\tSRS020226\tSRS020232\tSRS020233\tSRS020328\tSRS020334\tSRS020336\tSRS020340\tSRS020349\tSRS020386\tSRS020856\tSRS020858\tSRS020862\tSRS020869\tSRS022137\tSRS022143\tSRS022145\tSRS022149\tSRS022158\tSRS022524\tSRS022530\tSRS022532\tSRS022536\tSRS022545\tSRS022713\tSRS023346\tSRS023352\tSRS023358\tSRS042428\tSRS042457\tSRS042643\tSRS043001\tSRS043239\tSRS043663\tSRS043755\tSRS044366\tSRS044373\tSRS045004\tSRS045049\tSRS045254\tSRS045262\tSRS045313\tSRS045713\tSRS046344\tSRS046973\tSRS047824\tSRS048164\tSRS049389\tSRS049712\tSRS049900\tSRS049959\tSRS050007\tSRS050025\tSRS050029\tSRS050184\tSRS050244\tSRS050628\tSRS050752\tSRS051244\tSRS051505\tSRS051613\tSRS051941\tSRS052227\tSRS052330\tSRS052590\tSRS052604\tSRS052697\tSRS052876\tSRS053335\tSRS053398\tSRS053437\tSRS053630\tSRS053854\tSRS054061\tSRS054590\tSRS054653\tSRS054687\tSRS054956\tSRS055118\tSRS055401\tSRS056323\tSRS056695\tSRS056796\tSRS056906\tSRS057539\tSRS057791\tSRS057807\tSRS058186\tSRS058213\tSRS058808\r\n+STSite\tStool\tTongue_dorsum\tBuccal_mucosa\tSupragingival_plaque\tPosterior_fornix\tTongue_dorsum\tSupragingival_plaque\tAnterior_nares\tStool\tTongue_dorsum\tBuccal_mucosa\tSupragingival_plaq'..b'5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.000110565\t0\t0\t0\t0\t0\t0\t0\t0\t0.000105739\t0\t0\t0\t0\t2.33738e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.88647e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.39106e-05\t2.42838e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.000295775\t0\t0\t0\t0\t0\t6.81845e-06\t0\t0\t0\t0\t8.23749e-05\t0\t0\t0\t4.76472e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.12389e-06\t0\t0\t3.645e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Bulleidia.s__Bulleidia_extructa\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5.73523e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Campylobacter.s__Campylobacter_hominis\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.29465e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.14158e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Capnocytophaga.s__Capnocytophaga_sp_CM59\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.57568e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4.79523e-05\t0\t5.46675e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.45956e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.52358e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.65151e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Capnocytophaga.s__Capnocytophaga_sp_oral_taxon_338\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5.52837e-07\t0\t0\t0\t1.86027e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.5765e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.11797e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2.40718e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8.57993e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.324e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4.34332e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.88895e-06\t0\t0\t0\t0\t0\t4.18485e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.51934e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2.32256e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/rename_mapping --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rename_mapping Tue Aug 01 07:55:21 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +GO:0000015 GO1 +GO:0000049 GO2 +GO:0000179 GO3 +GO:0003697 GO4 +GO:0004594 GO5 +GO:0008137 GO6 + |
| b |
| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/rna_dna_norm-dna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_dna_norm-dna.txt Tue Aug 01 07:55:21 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# 1 2 +A 11 11 +A|1 10 10 +A|2 1 1 +D 5 10 +D|1 5 5 +D|2 0 5 |
| b |
| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/rna_dna_norm-rna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_dna_norm-rna.txt Tue Aug 01 07:55:21 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# 1 2 +A 22 22 +A|1 20 20 +A|2 2 22 +R 10 20 +R|1 10 10 +R|2 0 10 |
| b |
| diff -r dd4b5b9daf6b -r b6d4c448782f test-data/strain_profiler-input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strain_profiler-input.txt Tue Aug 01 07:55:21 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +HEADERS 1 2 3 +A 10 10 10 +A|g1.s1 10 10 10 +A|g1.s2 0 10 10 +B 10 10 10 +B|g1.s1 10 10 10 +B|g1.s2 10 0 10 +C 10 10 10 +C|g1.s1 10 10 0 +C|g1.s2 10 10 0 +C|g1.s3 10 10 10 |
