Mercurial > repos > bebatut > metaphlan2
changeset 31:83f06bee818c draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
| author | bebatut |
|---|---|
| date | Tue, 21 Feb 2017 12:29:37 -0500 |
| parents | 99fe591b59fb |
| children | c941148c75c7 |
| files | extract_markers.xml generate_test_data.sh merge_metaphlan_tables.xml metaphlan2.xml metaphlan2_macros.xml metaphlan2krona.xml metaphlan_hclust_heatmap.xml repository_dependencies.xml test-data/heatmap.pdf test-data/heatmap.png test-data/heatmap.svg test-data/merged_community_profile.tabular tool-data/metaphlan2_database.loc.sample tool-data/metaphlan2_db.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml transform_json_to_pkl.py |
| diffstat | 17 files changed, 1824 insertions(+), 82 deletions(-) [+] |
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--- /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 @@ +<tool id="metaphlan2_extract_markers" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0"> + + <description>output for Krona</description> + + <macros> + <import>metaphlan2_macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <version_command>extract_markers.py -v</version_command> + + <command> +<![CDATA[ + extract_markers.py + --mpa_pkl MPA_PKL + --ifn_markers IFN_MARKERS + --clade CLADE + --ofn_markers OFN_MARKERS +]]> + </command> + + <inputs> + <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/> + </inputs> + + <outputs> + <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" /> + </outputs> + + <tests> + <test> + <param name="input_file" value="community_profile.tabular"/> + <output name="krona" file="formatted_to_krona.tabular"/> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. + +This tool formats MetaPhlAn2 output to be ready for Krona. + + ]]></help> + + <expand macro="citations"/> +</tool>
--- /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
--- /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 @@ +<tool id="metaphlan2_merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0"> + + <description>MetaPhlAn2 files</description> + + <macros> + <import>metaphlan2_macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <version_command>merge_metaphlan_tables.py -v</version_command> + + <command> +<![CDATA[ + merge_metaphlan_tables.py + #for $element in $input_files + '$element' + #end for + > '$output' +]]> + </command> + + <inputs> + <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" /> + </inputs> + + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" /> + </outputs> + + <tests> + <test> + <param name="input_files" value="community_profile.tabular,community_profile.tabular"/> + <output name="output"> + <assert_contents> + <has_text text="#SampleID" /> + <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. + +This tool performs a table join on one or more metaphlan output files + + ]]></help> + + <expand macro="citations"/> +</tool>
--- 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 @@ -<tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0"> +<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0"> <description>to profile the composition of microbial communities</description> @@ -6,7 +6,10 @@ <import>metaphlan2_macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="2.2.5">bowtie2</requirement> + </expand> + <expand macro="stdio"/> <version_command> @@ -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' ]]> </command> <inputs> <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/> - <conditional name="db"> <param name="db_selector" type="select" label="Database with clade-specific marker genes" help=""> <option value="cached" selected="true">Locally cached</option> <option value="history">From history</option> </param> - <when value="cached"> <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" > - <options from_data_table="metaphlan2_db" /> + <options from_data_table="metaphlan2_database" /> </param> </when> <when value="history"> - <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/> - <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/> + <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> + <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> </when> </conditional> - <conditional name="analysis_type"> - <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)"> + <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t"> <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> + <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option> <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> </param> - <when value="rel_ab"> - <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output" help="(--tax_lev)"> + <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> <option value="a" selected="true">All taxonomic levels</option> <option value="k">Kingdoms (Bacteria and Archaea) only</option> <option value="p">Phyla only</option> @@ -115,46 +116,51 @@ <option value="s">Species only</option> </param> </when> - + <when value="rel_ab_w_read_stats"> + <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> + <option value="a" selected="true">All taxonomic levels</option> + <option value="k">Kingdoms (Bacteria and Archaea) only</option> + <option value="p">Phyla only</option> + <option value="c">Classes only</option> + <option value="o">Orders only</option> + <option value="f">Families only</option> + <option value="g">Genera only</option> + <option value="s">Species only</option> + </param> + </when> <when value="reads_map"/> <when value="clade_profiles"/> - <when value="marker_ab_table"> - <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/> + <param argument="--nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/> </when> - <when value="marker_counts"/> - <when value="marker_pres_table"> - <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/> + <param argument="--pres_th" type="integer" value="0" label=" Threshold for calling a marker present"/> </when> </conditional> - - <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/> - - <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/> - - <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" /> - <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" /> - - <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> - - <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" /> - - <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> + <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/> + <param argument="--min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/> + <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/> + <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/> + <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/> + <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/> + <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/> + <param argument="--sample_id_key" type="text" value="#SampleID" label="Sample ID key"/> + <param argument="--sample_id" type="text" value="Metaphlan2_Analysis" label="Sample ID"/> </inputs> <outputs> <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> + <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" /> </outputs> <tests> <test> <param name="input_file" value="input_sequences.fasta"/> <param name="db_selector" value="history" /> - <param name="db_metadata" value="marker_metadata.json" /> - <param name="db_sequences" value="marker_sequences.fasta" /> + <param name="mpa_pkl" value="marker_metadata.json" /> + <param name="bowtie2db" value="marker_sequences.fasta" /> <param name="analysis_type_select" value="rel_ab" /> <param name="taxonomic_level" value="a" /> <param name="min_cu_len" value="2000" /> @@ -164,6 +170,8 @@ <param name="ignore_bacteria" value="" /> <param name="ignore_archaea" value="" /> <param name="stat_q" value="0.1" /> + <param name="sample_id_key" value="#SampleID"/> + <param name="sample_id" value="Metaphlan2_Analysis"/> <output name="output_file" file="community_profile.tabular"/> </test> </tests> @@ -207,7 +215,5 @@ ]]></help> - <citations> - <citation type="doi">10.1038/nmeth.3589</citation> - </citations> + <expand macro="citations"/> </tool>
--- 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 @@ <?xml version="1.0"?> <macros> + <token name="@WRAPPER_VERSION@">2.6.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2.5">bowtie2</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="2.5.0">metaphlan2</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">metaphlan2</requirement> + <yield/> </requirements> </xml> <xml name="stdio"> @@ -20,4 +20,9 @@ description="" /> </stdio> </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3589</citation> + </citations> + </xml> </macros>
--- 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 @@ -<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0"> +<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0"> <description>output for Krona</description> @@ -9,22 +9,18 @@ <expand macro="requirements"/> <expand macro="stdio"/> - <version_command> -<![CDATA[ -metaphlan2krona.py -v -]]> - </version_command> + <version_command>metaphlan2krona.py -v</version_command> <command> <![CDATA[ metaphlan2krona.py - -p $input_file - -k $krona + --profile '$profile' + -k '$krona' ]]> </command> <inputs> - <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/> + <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/> </inputs> <outputs> @@ -33,7 +29,7 @@ <tests> <test> - <param name="input_file" value="community_profile.tabular"/> + <param name="profile" value="community_profile.tabular"/> <output name="krona" file="formatted_to_krona.tabular"/> </test> </tests> @@ -48,7 +44,5 @@ ]]></help> - <citations> - <citation type="doi">10.1038/nmeth.3589</citation> - </citations> + <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan_hclust_heatmap.xml Tue Feb 21 12:29:37 2017 -0500 @@ -0,0 +1,276 @@ +<tool id="metaphlan2_metaphlan_hclust_heatmap" name="Generate heatmap" version="@WRAPPER_VERSION@.0"> + + <description>with hierarchical clustering of both samples +and microbial clades for MetaPhlAn2</description> + + <macros> + <import>metaphlan2_macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <version_command>metaphlan_hclust_heatmap.py -v</version_command> + + <command> +<![CDATA[ + metaphlan_hclust_heatmap.py + --in '$in' + + #if $output_format == "png" + --out 'output.png' + #else if $output_format == "pdf" + --out 'output.pdf' + #else if $output_format == "svg" + --out 'output.svg' + #end if + + -m '$m' + -d '$d' + -f '$f' + + #if $x + -x '$x' + #end if + #if $y + -y '$y' + #end if + --minv '$minv' + #if $maxv + --maxv $maxv + #end if + --tax_lev '$tax_lev' + --perc '$perc' + #if $top + --top '$top' + #end if + --sdend_h '$sdend_h' + --fdend_w '$fdend_w' + --cm_h '$cm_h' + --font_size '$font_size' + --clust_line_w '$clust_line_w' + -c '$c' +]]> + </command> + + <inputs> + <param argument="--in" type="data" format="tabular,txt" label="Input file of microbial relative abundances" help="This file is typically obtained with merge_metaphlan_tables"/> + <param name="output_format" type="select" label="Format for the output image"> + <option value="png" selected="true">PNG</option> + <option value="pdf">PDF</option> + <option value="svg">SVG</option> + </param> + <param argument="-m" type="select" label="Hierarchical clustering method"> + <option value="average" selected="true">Average</option> + <option value="centroid">Centroid</option> + <option value="complete">Complete</option> + <option value="median">Median</option> + <option value="single">Single</option> + <option value="ward">Ward</option> + <option value="weighted">Weighted</option> + </param> + <param argument="-d" type="select" label="Distance function for samples"> + <option value="braycurtis" selected="true">braycurtis</option> + <option value="canberra">canberra</option> + <option value="chebyshev">chebyshev</option> + <option value="cityblock">cityblock</option> + <option value="correlation">correlation</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="euclidean">euclidean</option> + <option value="hamming">hamming</option> + <option value="jaccard">jaccard</option> + <option value="kulsinski">kulsinski</option> + <option value="mahalanobis">mahalanobis</option> + <option value="matching">matching</option> + <option value="minkowski">minkowski</option> + <option value="rogerstanimoto">rogerstanimoto</option> + <option value="russellrao">russellrao</option> + <option value="seuclidean">seuclidean</option> + <option value="sokalmichener">sokalmichener</option> + <option value="sokalsneath">sokalsneath</option> + <option value="sqeuclidean">sqeuclidean</option> + <option value="wminkowski">wminkowski</option> + <option value="ward">ward</option> + <option value="yule">yule</option> + </param> + <param argument="-f" type="select" label="Distance function for microbes"> + <option value="braycurtis">braycurtis</option> + <option value="canberra">canberra</option> + <option value="chebyshev">chebyshev</option> + <option value="cityblock">cityblock</option> + <option value="correlation" selected="true">correlation</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="euclidean">euclidean</option> + <option value="hamming">hamming</option> + <option value="jaccard">jaccard</option> + <option value="kulsinski">kulsinski</option> + <option value="mahalanobis">mahalanobis</option> + <option value="matching">matching</option> + <option value="minkowski">minkowski</option> + <option value="rogerstanimoto">rogerstanimoto</option> + <option value="russellrao">russellrao</option> + <option value="seuclidean">seuclidean</option> + <option value="sokalmichener">sokalmichener</option> + <option value="sokalsneath">sokalsneath</option> + <option value="sqeuclidean">sqeuclidean</option> + <option value="wminkowski">wminkowski</option> + <option value="ward">ward</option> + <option value="yule">yule</option> + </param> + <param argument="-x" type="integer" optional="True" label="Width of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/> + <param argument="-y" type="integer" optional="True" label="Height of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/> + <param argument="--minv" type="float" value="0" label="Minimum value to display" help="Values around 0.001 are also reasonable"/> + <param argument="--maxv" type="float" optional="True" label="Maximum value to display" help="Default is maximum value present, can be set e.g. to 100 to display the full scale"/> + <param argument="--tax_lev" type="select" label="Taxonomic level to display"> + <option value="a">All taxonomic levels</option> + <option value="k">Kingdoms (Bacteria and Archaea) only</option> + <option value="p">Phyla only</option> + <option value="c">Classes only</option> + <option value="o">Orders only</option> + <option value="f">Families only</option> + <option value="g">Genera only</option> + <option value="s" selected="true">Species only</option> + </param> + <param argument="--perc" type="integer" value="90" label="Percentile to be used for ordering the microbes"/> + <param argument="--top" type="integer" optional="True" label="Number of most abundant microbes to display"/> + <param argument="--sdend_h" type="float" value="0.1" label="Height of the sample dendrogram"/> + <param argument="--fdend_w" type="float" value="0.1" label="Width of the sample dendrogram"/> + <param argument="--cm_h" type="float" value="0.03" label="Height of the colormap"/> + <param argument="--font_size" type="integer" value="7" label="Label font sizes"/> + <param argument="--clust_line_w" type="float" value="" label="Line width for the dendrograms"/> + <param argument="-c" type="select" label="Taxonomic level to display"> + <option value="autumn">autumn</option> + <option value="bbcyr">bbcyr</option> + <option value="bbcry">bbcry</option> + <option value="binary">binary</option> + <option value="Blues">Blues</option> + <option value="bone">bone</option> + <option value="BrBG">BrBG</option> + <option value="brg">brg</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="bwr">bwr</option> + <option value="cool">cool</option> + <option value="copper">copper</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_stern">gist_stern</option> + <option value="GnBu">GnBu</option> + <option value="gray">gray</option> + <option value="Greys">Greys</option> + <option value="hot">hot</option> + <option value="hsv">hsv</option> + <option value="jet" selected="true">jet</option> + <option value="OrRd">OrRd</option> + <option value="Oranges">Oranges</option> + <option value="PRGn">PRGn</option> + <option value="pink">pink</option> + <option value="PiYG">PiYG</option> + <option value="PuBu">PuBu</option> + <option value="PuBuGn">PuBuGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="Purples">Purples</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="RdYlBu">RdYlBu</option> + <option value="RdYlGn">RdYlGn</option> + <option value="Reds">Reds</option> + <option value="seismic">seismic</option> + <option value="spectral">spectral</option> + <option value="Spectral">Spectral</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="terrain">terrain</option> + <option value="winter">winter</option> + <option value="YlGn">YlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + </param> + </inputs> + + <outputs> + <data format="pdf" name="out_pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}"> + <filter>output_format == "pdf"</filter> + </data> + <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string}"> + <filter>output_format == "png"</filter> + </data> + <data format="svg" name="out_svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}"> + <filter>output_format == "svg"</filter> + </data> + </outputs> + + <tests> + <test> + <param name="in" value="merged_community_profile.tabular"/> + <param name="output_format" value="png"/> + <param name="m" value="average"/> + <param name="d" value="braycurtis"/> + <param name="f" value="correlation"/> + <param name="minv" value="0"/> + <param name="tax_lev" value="a"/> + <param name="perc" value="90"/> + <param name="sdend_h" value="0.1"/> + <param name="fdend_w" value="0.1"/> + <param name="cm_h" value="0.03"/> + <param name="font_size" value="7"/> + <param name="clust_line_w" value="1"/> + <param name="c" value="jet"/> + <output name="out_png" file="heatmap.png" lines_diff='5'/> + </test> + <test> + <param name="in" value="merged_community_profile.tabular"/> + <param name="output_format" value="pdf"/> + <param name="m" value="ward"/> + <param name="d" value="euclidean"/> + <param name="f" value="euclidean"/> + <param name="minv" value="0"/> + <param name="tax_lev" value="a"/> + <param name="perc" value="90"/> + <param name="sdend_h" value="0.1"/> + <param name="fdend_w" value="0.1"/> + <param name="cm_h" value="0.03"/> + <param name="font_size" value="7"/> + <param name="clust_line_w" value="1"/> + <param name="c" value="pink"/> + <output name="out_pdf" md5="35702e08d994cd64371cdce3e025dc5a"/> + </test> + <test> + <param name="in" value="merged_community_profile.tabular"/> + <param name="output_format" value="svg"/> + <param name="m" value="complete"/> + <param name="d" value="hamming"/> + <param name="f" value="matching"/> + <param name="minv" value="0"/> + <param name="tax_lev" value="a"/> + <param name="perc" value="90"/> + <param name="sdend_h" value="0.1"/> + <param name="fdend_w" value="0.1"/> + <param name="cm_h" value="0.03"/> + <param name="font_size" value="7"/> + <param name="clust_line_w" value="1"/> + <param name="c" value="pink"/> + <output name="out_svg" md5="844799aca7af03db2c2f6222b873c8cf"/> + </test> + </tests> + + <help><![CDATA[ + +**What it does** + +MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. + +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 + + ]]></help> + + <expand macro="citations"/> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases."> + <repository changeset_revision="332cb1b3b349" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>
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--- /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
--- /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
--- 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
--- 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 @@ <tables> - <table name="metaphlan2_db" comment_char="#"> + <table name="metaphlan2_database" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/metaphlan2_db.loc" /> + <file path="tool-data/metaphlan2_database.loc" /> </table> </tables>
--- 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 @@ <?xml version="1.0"?> <tool_dependency> <package name="numpy" version="1.9"> - <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="bowtie2" version="2.2.5"> <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
--- 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)