Mercurial > repos > drosofff > msp_sr_size_histograms
changeset 2:a95419680ce4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6
| author | drosofff |
|---|---|
| date | Thu, 10 Mar 2016 11:00:00 -0500 |
| parents | 00852209fd9f |
| children | 31782dbb7d85 |
| files | size_histogram.xml tool_dependencies.xml |
| diffstat | 2 files changed, 166 insertions(+), 144 deletions(-) [+] |
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--- a/size_histogram.xml Wed Oct 21 11:50:42 2015 -0400 +++ b/size_histogram.xml Thu Mar 10 11:00:00 2016 -0500 @@ -1,99 +1,99 @@ -<tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.7"> - <description>from sRbowtie aligment</description> - <requirements> +<tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.8"> + <description>from sRbowtie aligment</description> + <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> <requirement type="package" version="0.7.7">pysam</requirement> <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="2.14">biocbasics</requirement> <requirement type="package" version="1.9">numpy</requirement> - </requirements> -<command interpreter="python"> - size_histogram.py - #if $refGenomeSource.genomeSource == "history": - --reference_fasta ## sys.argv[2] - $refGenomeSource.ownFile ## index source - #else: - #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - --reference_bowtie_index - $reference - #end if - --rcode - $plotCode - --output_size_distribution - $size_distribution_dataframe - --minquery - $minquery - --maxquery - $maxquery - --input - #for $i in $refGenomeSource.series - $i.input - #end for - --ext - #for $i in $refGenomeSource.series - $i.input.ext - #end for - --label - #for $i in $refGenomeSource.series - "$i.input.name" - #end for - --normalization_factor - #for $i in $refGenomeSource.series - $i.norm - #end for - #if $gff: - --gff - $gff - #end if - #if $global.value == 'yes': - --global_size - #end if - #if $collapsestrands.value == 'yes': - --collapse - #end if + </requirements> + <command interpreter="python"> + size_histogram.py + #if $refGenomeSource.genomeSource == "history": + --reference_fasta ## sys.argv[2] + $refGenomeSource.ownFile ## index source + #else: + #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] + --reference_bowtie_index + $reference + #end if + --rcode + $plotCode + --output_size_distribution + $size_distribution_dataframe + --minquery + $minquery + --maxquery + $maxquery + --input + #for $i in $refGenomeSource.series + $i.input + #end for + --ext + #for $i in $refGenomeSource.series + $i.input.ext + #end for + --label + #for $i in $refGenomeSource.series + "$i.input.name" + #end for + --normalization_factor + #for $i in $refGenomeSource.series + $i.norm + #end for + #if $gff: + --gff $gff + #end if + #if $global.value == 'yes': + --global_size + #end if + #if $collapsestrands.value == 'yes': + --collapse + #end if -</command> - <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <repeat name="series" title="Add alignment files"> - <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> - <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> - </param> - <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> - </repeat> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> - <repeat name="series" title="Add alignment files"> - <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> - <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> - </repeat> - </when> - </conditional> - <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> - <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> - <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment"> - <option value="no">for each item</option> - <option value="yes">global</option> - </param> - <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not"> - <option value="no">Do not collapse</option> - <option value="yes">Collapse + and - reads</option> - </param> - <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/> - <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/> - <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/> - <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/> - <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> - <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> - <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> - </param> - </inputs> + </command> + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <repeat name="series" title="Add alignment files"> + <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> + <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> + </param> + <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> + </repeat> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> + <repeat name="series" title="Add alignment files"> + <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> + <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> + </repeat> + </when> + </conditional> + <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> + <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> --> + <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment"> + <option value="no">for each item</option> + <option value="yes">global</option> + </param> + <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not"> + <option value="no">Do not collapse</option> + <option value="yes">Collapse + and - reads</option> + </param> + <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/> + <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/> + <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/> + <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/> + <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/> + <param name="yrange" type="integer" size="3" value="0" label="y axis range for size distributions. 0 means auto-scaling."/> + <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?"> + <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/> + </param> + </inputs> <configfiles> <configfile name="plotCode"> ## Setup R error handling to go to stderr @@ -110,6 +110,11 @@ n_samples = length(unique (size\$sample)) n_genes = length (unique (levels(size\$gene))) + if (${yrange} != 0) { + # This is used for specifying the y-axis limits + ylim=c(-${yrange}, ${yrange}) + } else { ylim="" } + par.settings.size=list(layout.heights=list(top.padding=1, bottom.padding=1), strip.background = list(col = c("lightblue", "lightgreen")) ) @@ -132,7 +137,7 @@ newpage = T, ...) - combineLimits(update(useOuterStrips(bc, + combineLimits(update(useOuterStrips(bc, strip.left = strip.custom(par.strip.text = list(cex=0.5)) ), layout=c(n_samples,${rows_per_page})), @@ -147,44 +152,61 @@ #end if if (global=="no") { + width = 8.2677*n_samples/4 + } else { width = 8.2677 } options(warn=-1) - pdf(file="${size_PDF}", paper="special", height=11.69, width=8.2677*n_samples/4) - plot_size_distribution(size, par.settings=par.settings.size) # removed , prepanel=smR.prepanel - - } else { + pdf(file="${size_PDF}", paper="special", height=11.69, width=width) - pdf(file="${size_PDF}", paper="special", height=11.69, width=8.2677) - bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)), data = size, origin = 0, - horizontal=FALSE, - group=polarity, - stack=TRUE, - col=c('red', 'blue'), -# par.settings=list(fontsize = list(text=8, points=8)), - scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1), - xlab = "readsize in nucleotides", - ylab = "${ylabel}", - main="${title}" , as.table=TRUE, newpage = T, - aspect=0.5, - strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue") - ) - bc - } + if (ylim == "" && global=="no") { + plot_size_distribution(size, par.settings=par.settings.size) + } + if (ylim != "" && global=="no") { plot_size_distribution(size, par.settings=par.settings.size, ylim=ylim) + } + if (ylim == "" && global=="yes") { bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)), data = size, origin = 0, + horizontal=FALSE, + group=polarity, + stack=TRUE, + col=c('red', 'blue'), + scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1), + xlab = "readsize in nucleotides", + ylab = "${ylabel}", + main="${title}" , as.table=TRUE, newpage = T, + aspect=0.5, + strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue") + ) + bc + } + if (ylim != "" && global=="yes") { bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)), data = size, origin = 0, + horizontal=FALSE, + group=polarity, + stack=TRUE, + col=c('red', 'blue'), + scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1), + xlab = "readsize in nucleotides", + ylab = "${ylabel}", + ylim = ylim, + main="${title}" , as.table=TRUE, newpage = T, + aspect=0.5, + strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue") + ) + bc + } + devname=dev.off() </configfile> </configfiles> - - <outputs> - <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/> - <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/> - </outputs> + <outputs> + <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/> + <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/> + </outputs> <help> **What it does** -Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes, -where by default for each "chromosome" a histogram of read sizes is drawn. +Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes, +where by default for each "chromosome" a histogram of read sizes is drawn. Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue). @@ -209,32 +231,32 @@ ---- -.. image:: static/images/size_histogram.png - :height: 800 +.. image:: static/images/size_histogram.png + :height: 800 :width: 500 </help> - <tests> - <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="transposons.fasta" ftype="fasta" /> - <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> - <param name="series_0|norm" value="1" /> - <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> - <param name="series_1|norm" value="1" /> - <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> - <param name="series_2|norm" value="1" /> - <param name="global" value="no" /> - <param name="collapsestrands" value="no" /> - <param name="minquery" value="18"/> - <param name="maxquery" value="30"/> - <param name="title" value="Size distribution"/> - <param name="xlabel" value="Size in nucleotides"/> - <param name="ylabel" value="Number of reads"/> - <param name="rows_per_page" value="10"/> - <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> - <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" /> - </test> - </tests> + <tests> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="transposons.fasta" ftype="fasta" /> + <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> + <param name="series_0|norm" value="1" /> + <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> + <param name="series_1|norm" value="1" /> + <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> + <param name="series_2|norm" value="1" /> + <param name="global" value="no" /> + <param name="collapsestrands" value="no" /> + <param name="minquery" value="18"/> + <param name="maxquery" value="30"/> + <param name="title" value="Size distribution"/> + <param name="xlabel" value="Size in nucleotides"/> + <param name="ylabel" value="Number of reads"/> + <param name="rows_per_page" value="10"/> + <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> + <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" /> + </test> + </tests> </tool>
--- a/tool_dependencies.xml Wed Oct 21 11:50:42 2015 -0400 +++ b/tool_dependencies.xml Thu Mar 10 11:00:00 2016 -0500 @@ -7,10 +7,10 @@ <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> - <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c8f7a7d73466" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="biocbasics" version="2.14"> <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />