Mercurial > repos > bebatut > metaphlan2
changeset 38:4d1bf99ad5ef draft
Uploaded
| author | bebatut |
|---|---|
| date | Mon, 27 Feb 2017 06:12:35 -0500 |
| parents | e7ed163633e1 |
| children | 99066fa0645b |
| files | merge_metaphlan_tables.xml metaphlan2.xml metaphlan2krona.xml metaphlan_hclust_heatmap.xml |
| diffstat | 4 files changed, 1 insertions(+), 380 deletions(-) [+] |
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--- a/merge_metaphlan_tables.xml Thu Feb 23 08:13:41 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -<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 Feb 23 08:13:41 2017 -0500 +++ b/metaphlan2.xml Mon Feb 27 06:12:35 2017 -0500 @@ -42,7 +42,7 @@ --bowtie2_exe `which bowtie2` #if $db.db_selector == "cached" - #set $path = ${db.cached_db.fields.path} + #set $path = $db.cached_db.fields.path --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'` --mpa_pkl `ls $path/*.pkl` #else
--- a/metaphlan2krona.xml Thu Feb 23 08:13:41 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0"> - - <description>output for Krona</description> - - <macros> - <import>metaphlan2_macros.xml</import> - </macros> - - <expand macro="requirements"/> - <expand macro="stdio"/> - - <version_command>metaphlan2krona.py -v</version_command> - - <command> -<![CDATA[ - metaphlan2krona.py - --profile '$profile' - -k '$krona' -]]> - </command> - - <inputs> - <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/> - </inputs> - - <outputs> - <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" /> - </outputs> - - <tests> - <test> - <param name="profile" value="community_profile.tabular"/> - <output name="krona" file="formatted_to_krona.tabular"/> - </test> - </tests> - - <help><![CDATA[ - -**What it does** - -MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. - -This tool formats MetaPhlAn2 output to be ready for Krona. - - ]]></help> - - <expand macro="citations"/> -</tool>
--- a/metaphlan_hclust_heatmap.xml Thu Feb 23 08:13:41 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,276 +0,0 @@ -<tool id="metaphlan2_metaphlan_hclust_heatmap" name="Generate heatmap" version="@WRAPPER_VERSION@.0"> - - <description>with hierarchical clustering of both samples -and microbial clades for MetaPhlAn2</description> - - <macros> - <import>metaphlan2_macros.xml</import> - </macros> - - <expand macro="requirements"/> - <expand macro="stdio"/> - - <version_command>metaphlan_hclust_heatmap.py -v</version_command> - - <command> -<![CDATA[ - metaphlan_hclust_heatmap.py - --in '$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" ftype="png" compare="sim_size"/> - </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" file="heatmap.pdf" compare="sim_size"/> - </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" file="heatmap.svg" ftype="svg" compare="sim_size"/> - </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>