Mercurial > repos > iuc > intervene
changeset 0:f5fa293605ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene commit 9b67be72f7330b1b9af7944aa695c9f5d6d20a15
| author | iuc |
|---|---|
| date | Wed, 12 Sep 2018 13:22:43 -0400 |
| parents | |
| children | 08780101bc36 |
| files | intervene_pairwise.xml intervene_upset.xml macros.xml static/images/pairwise.png static/images/upset.png test-data/a.bed test-data/a.txt test-data/b.bed test-data/b.txt test-data/bed_pairwise.pdf test-data/bed_upset.pdf test-data/c.bed test-data/c.txt test-data/upset.pdf |
| diffstat | 14 files changed, 252 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/intervene_pairwise.xml Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,96 @@ +<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@"> + <description>and heatmap for genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">intervene</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +#import re +#set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input]) +#set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list' +intervene pairwise +--type $type +--input #echo " ".join(["'%s'" % file for file in $input]) +--names $labels +--compute $compute +#if str($corrtype) != 'None' + --corr + --corrtype $corrtype +#end if +--htype $htype +$diagonal +--output results +--barcolor '$barcolor' +--fontsize '$fontsize' +--title '$title' +--figtype $figtype +--figsize $figsize_width $figsize_height +--dpi $dpi && +mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot + ]]></command> + <inputs> + <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/> + <param argument="--compute" type="select" label="Use this metric for the heatmap"> + <option value="count">count: calculates the number of overlaps</option> + <option value="frac" selected="true">frac: calculates the fraction of overlap</option> + <option value="jaccard">jaccard: calculate the Jaccard statistic</option> + <option value="reldist">reldist: calculate the distribution of relative distances</option> + <!-- fisher option needs additional genome assembly, probably triggers on demand download + <option value="fisher">fisher: calculate Fisher`s statistic</option> + --> + </param> + <param argument="--corrtype" type="select" label="Select the type of correlation"> + <option value="None">Don't calculate correlation</option> + <option value="pearson">Pearson correlation</option> + <option value="kendall">Kendall correlation</option> + <option value="spearman">Spearman correlation</option> + </param> + <param argument="--htype" type="select" label="Heatmap plot type"> + <option value="tribar">tribar</option> + <option value="dendrogram">dendrogram</option> + <option value="color">color</option> + <option value="pie">pie</option> + <option value="circle">circle</option> + <option value="square">square</option> + <option value="ellipse">ellipse</option> + <option value="number">number</option> + <option value="shade">shade</option> + </param> + <param argument="--diagonal" type="boolean" truevalue="--diagonal" falsevalue="" label="Show the diagonal values in the heatmap ?"/> + <!-- the argparse action is wrong for showsize, check this when upgrading tool in future --> + <param argument="--barcolor" type="color" label="Boxplot color" value="#53cfff"> + <expand macro="color_sanitizer"/> + </param> + <param argument="--fontsize" type="integer" value="8" label="Label font size"/> + <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection"> + <expand macro="quote_sanitizer"/> + </param> + <expand macro="figure_params"/> + </inputs> + <outputs> + <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot"> + <actions> + <action type="format"> + <option type="from_param" name="figtype"/> + </action> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input" value="a.bed,b.bed,c.bed"/> + <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Plots the pairwise intersections of multiple interval files. + +.. image:: $PATH_TO_IMAGES/pairwise.png + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/intervene_upset.xml Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,84 @@ +<tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@"> + <description>of intersection of genomic regions or list sets</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">intervene</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +#import re +#set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input]) +#set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list' +intervene upset +--type $type +--input #echo " ".join(["'%s'" % file for file in $input]) +--names $labels +--output results +--order $order +--ninter $ninter +$showzero +$showsize +--mbcolor '$mbcolor' +--sbcolor '$sbcolor' +--mblabel '$mblabel' +--sxlabel '$sxlabel' +--figtype $figtype +--figsize $figsize_width $figsize_height +--dpi $dpi && +mv results/Intervene_upset.${figtype} results/Intervene_upset.plot + ]]></command> + <inputs> + <param argument="--input" type="data" format="txt" multiple="true" label="Select input files for which to produce intersections"/> + <param argument="--order" type="select" label="Select the order of intersections of sets"> + <option value="freq">Frequency</option> + <option value="degree">Degree</option> + </param> + <param argument="--ninter" type="integer" value="30" min="1" label="Number of top intersections to show in plot"/> + <param argument="--showzero" type="boolean" truevalue="--showzero" falsevalue="" label="Show empty intersections in plot?"/> + <!-- the argparse action is wrong for showsize, check this when upgrading tool in future --> + <param argument="--showsize" type="boolean" truevalue="" falsevalue="--showsize" checked="true" label="Show intersection sizes above bars ?"/> + <param argument="--mbcolor" type="color" label="Color of the main bar plot" value="#ea5d4e"> + <expand macro="color_sanitizer"/> + </param> + <param argument="--sbcolor" type="color" label="Color of the set size bar plot" value="#317eab"> + <expand macro="color_sanitizer"/> + </param> + <param argument="--mblabel" type="text" label="The y-axis label of the intersection size bars" value="No. of Intersections"> + <expand macro="quote_sanitizer"/> + </param> + <param argument="--sxlabel" type="text" label="The x-axis label of the set size bars" value="Set size"> + <expand macro="quote_sanitizer"/> + </param> + <expand macro="figure_params"/> + </inputs> + <outputs> + <data name="plot" format="pdf" label="UpSet plot on ${on_string}" from_work_dir="results/Intervene_upset.plot"> + <actions> + <action type="format"> + <option type="from_param" name="figtype"/> + </action> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input" value="a.txt,b.txt,c.txt"/> + <output name="plot" value="upset.pdf" compare="sim_size"/> + </test> + <test> + <param name="input" value="a.bed,b.bed,c.bed"/> + <output name="plot" value="bed_upset.pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool produces an upset plot for the intersection of sets from different datasets. +These can be regular lists or BED/GFF/interval files which will be processed using bedtools intersect. + +.. image:: $PATH_TO_IMAGES/upset.png + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,35 @@ +<macros> + <xml name="color_sanitizer"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </xml> + <xml name="quote_sanitizer"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + </sanitizer> + </xml> + <xml name="figure_params"> + <param argument="--figtype" type="select" label="Select figure type for plot"> + <option value="pdf">pdf</option> + <option value="svg">svg</option> + <option value="ps">ps</option> + <option value="tiff">tiff</option> + <option value="png">png</option> + </param> + <param name="figsize_width" type="integer" value="14" min="2" label="Width of the output plot"/> + <param name="figsize_height" type="integer" value="8" min="2" label="Height of the output plot"/> + <param argument="--dpi" type="integer" value="300" min="60" max="1200" label="Dots-per-inch (DPI) for the output"/> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12859-017-1708-7</citation> + </citations> + </xml> + <token name="@TOOL_VERSION@">0.6.4</token> + <token name="@ESCAPE_IDENTIFIER@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.bed Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,8 @@ +chr1 0 1000 +chr1 1000 1500 +chr1 1500 1980 +chr1 1980 2000 +chr1 2000 2070 +chr1 2070 2090 +chr1 2090 2100 +chr1 2100 5000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.txt Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,5 @@ +A +B +C +D +E
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b.bed Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,6 @@ +chr1 0 1000 +chr1 1000 1500 +chr1 1500 1980 +chr1 2070 2090 +chr1 2090 2100 +chr1 2100 5000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b.txt Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,8 @@ +A +B +C +D +E +F +G +H
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/c.bed Wed Sep 12 13:22:43 2018 -0400 @@ -0,0 +1,7 @@ +chr1 0 1000 +chr1 1500 1980 +chr1 1980 2000 +chr1 2000 2070 +chr1 2070 2090 +chr1 2090 2100 +chr1 2100 5000