Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 45:ee7209928db8 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 27 Jan 2016 05:35:55 -0500 |
| parents | 4c5033eb708f |
| children | fee06348bfad |
| files | complete.sh report_clonality/circos/circos.conf report_clonality/circos/housekeeping.conf report_clonality/r_wrapper.sh |
| diffstat | 4 files changed, 264 insertions(+), 26 deletions(-) [+] |
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--- a/complete.sh Tue Jan 26 10:10:04 2016 -0500 +++ b/complete.sh Wed Jan 27 05:35:55 2016 -0500 @@ -53,10 +53,6 @@ count=$((count+1)) done -echo "<tr><td>after loooop</td></tr>" >> $html - -echo "after loop" - echo "<tr><td>-----------------------------------</td></tr>" >> $html echo "<tr><td>merging</td></tr>" >> $html
--- a/report_clonality/circos/circos.conf Tue Jan 26 10:10:04 2016 -0500 +++ b/report_clonality/circos/circos.conf Wed Jan 27 05:35:55 2016 -0500 @@ -134,13 +134,15 @@ </links> -anglestep = 0.5 -minslicestep = 10 -beziersamples = 40 -debug = no -warnings = no -imagemap = no +#anglestep = 0.5 +#minslicestep = 10 +#beziersamples = 40 +#debug = no +#warnings = no +#imagemap = no -units_ok = bupr -units_nounit = n +#units_ok = bupr +#units_nounit = n +<<include DATA_DIR/housekeeping.conf>> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/circos/housekeeping.conf Wed Jan 27 05:35:55 2016 -0500 @@ -0,0 +1,230 @@ +# Housekeeping parameters, which must be included +# at the top level of the configuration. +# +# Don't adjust these, unless you know what you are doing, or +# feel like experimenting + +anglestep = 0.5 +minslicestep = 10 +beziersamples = 40 # bezier curves are drawn piece-wise + # linear, with this many samples +debug = no +warnings = no +imagemap = no +paranoid = yes + +units_ok = bupr +units_nounit = n + +# \t tab +# \s any whitespace +file_delim = \s +# collapse adjacent whitespace +# e.g. two spaces are treated as one, not as a missing field +file_delim_collapse = yes + +# Record delimiter for parameter values that are lists, such as +# hs1:0.25;hs2:0.10. By default, both ; and , are accepted +# +# e.g. hs1:0.25,hs2:0.10 +# hs1:0.25;hs2:0.10 +list_record_delim = \s*[;,]\s* +# Field delimiter specifies the assignment operator, e.g. +list_field_delim = \s*[:=]\s*] + +# Rule fields and other parameters accept var(VARIABLE) syntax +# to reference parameters of data points. By default, if +# VARIABLE does not exist, Circos quits with an error, unless +# the skip parameter below is set. +# +# This feature is useful when you have data that don't always +# have the same options. For example, +# +# chr1 10 20 a=10 +# chr1 50 60 b=10 +skip_missing_expression_vars = no + +# In old versions, data point parameters were referenced using _NAME_ +# syntax. This has been replaced with var(NAME). The _NAME_ syntax is +# deprecated (for example, it will break when dealing with fields like +# gene_a_1). If you must use it, set the parameter below. + +legacy_underline_expression_syntax = no + +# Magnification factor for text in SVG files. +svg_font_scale = 1.3 + +# default font - pick one of the keys from <fonts> block +default_font = default +# default font name is used for SVG files for cases where +# the font definition does not include a name +# see etc/fonts.conf for details +default_font_name = Arial +default_font_color = black + +# default color for cases when color is not specified +default_color = black + +<guides> +thickness = 1 +size = 5 +type = outline +<object> +all = no +ideogram = no +ideogram_label = no +</object> +<color> +default = lblue +text = red +</color> +</guides> + +# Receive debug messages about actions +# +# Comma-separated list of one or more of the following +# +# summary - top level indications of what's happening +# chrfilter - ideogram filtering (parsing 'chromosomes' parameter) +# conf - configuration file +# counter - plot counters +# spacing - ideogram spacing +# scale - ideogram scaling +# ideogram - ideogram reporting +# anglepos - report angle positions for base pair coordinates +# zoom - zoom regions +# layers - specific plot z-layers +# rules - dynamic rules +# text - text tracks +# heatmap - detailed heatmap reports +# brush - brushes +# color - color allocation and definition +# ticks - tick marks and labels +# timers - some benchmark timings +# cache - caches +# _all - turn on all groups +debug_group = summary + +# run length duration after which timing report is automatically +# generated at the end of the run +debug_auto_timer_report = 30 + +debug_word_separator = " " +debug_undef_text = _undef_ +debug_empty_text = _emptylist_ + +# parameters passed to functions can be +# validated to check consistency. turn this +# off to speed things up +debug_validate = yes + +# Reformat numbers in debug output for consistency. +# If you have a lot of debug output (e.g. -debug_group _all) +# this will slow things considerably. +debug_output_tidy = no + +# pixel sub-sampling for text tracks +text_pixel_subsampling = 1 +# array or span - use 'span' if applying snuggle refinement +text_snuggle_method = array + +# restrict names of parameters? +# if 'yes' then only certain named parameters are allowed within +# blocks and option fields for data +# +# if 'no' then you can define parameters with any name what-so-ever, +# useful if you wish to define states or labels for your data +# +# e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5 +# +# ordinarily, 'paired', 'special' and 'myvar' would not be allowed +restrict_parameter_names = no + +# Unless set to 'yes', parameter names will be converted to lowercase +case_sensitive_parameter_names = no + +# The location of configuration and data files will be guessed if +# (a) configuration file is not specified +# (b) data file paths are relative +# Circos will look in the following locations, where +# SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and +# CWD is the current directory (where the 'circos' command was executed). +# All paths under CWD will be scanned first, then under SCRIPTPATH. +# +# {CWD,SCRIPTPATH}/. +# {CWD,SCRIPTPATH}/.. +# {CWD,SCRIPTPATH}/etc/ +# {CWD,SCRIPTPATH}/../etc +# {CWD,SCRIPTPATH}/../../etc +# {CWD,SCRIPTPATH}/data +# {CWD,SCRIPTPATH}/../data +# {CWD,SCRIPTPATH}/../../data +# +# If you would like to prepend this list with custom directories for +# data files, enter them as a CSV list here +# data_path = /home/martink/circos-tutorials +# If the cache is static, it will always be used and will not be updated +# unless it is deleted (use -color_cache_rebuild on the command line). +# Otherwise, the cache will be updated if +# - config file is newer than cache file +# - list of colors in config file is different than in cache file +color_cache_static = yes +color_cache_file = circos.colorlist +color_lists_use = yes +# if the directory is not defined, then the system will guess a temporary +# directory compatible with your operating system (using File::Temp) +# color_cache_dir = /tmp + +# Make some functions faster. This should always be 'yes' unless you +# want things to run slowly or suspect deep issues. +memoize = yes + +# This is a debugging flag and should be set to 'no' for regular use +quit_on_dump = yes + +offsets = 0,0 + +# Maximum number of image and data elements. If these are exceeded, +# Circos will quit with an error. These values are arbitrary, but in +# my experience images with significantly more data points than this +# are uninterpretable. + +max_ticks = 5000 +max_ideograms = 200 +max_links = 25000 +max_points_per_track = 25000 + +# What to do when data is found for an ideogram that does not appear in the karyotype file. + +# Set to 'skip' or 'exit' +undefined_ideogram = skip + +# Number of iterations for determining ideogram sizes when +# relative scale is used. +relative_scale_iterations = 10 + +# min, max, average, mode - based on scale statistics of ALL ideograms +# minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms +# +# You can specify a fixed scale for spacing using a floating value +# +# e.g. relative_scale_spacing = 1.5 +relative_scale_spacing = mode + +# What to do with out-of-range data. Either 'clip' or 'hide' +data_out_of_range = clip + +# Track default directory +track_defaults = etc/tracks + +# Use round brushes for elements with thickness greater than round_brush_min_thickness? +round_brush_use = yes +round_brush_min_thickness = 5 + +# Use anti aliasing, where possible? I've seen bugs in some gd libraries +# that cause artefacts to appear when lines are anti-aliased. If your +# image contains unexpected elements, turn aa off. +anti_aliasing = yes + +# A parameter that must be set. Checks whether this file was imported. +housekeeping = yes
--- a/report_clonality/r_wrapper.sh Tue Jan 26 10:10:04 2016 -0500 +++ b/report_clonality/r_wrapper.sh Wed Jan 27 05:35:55 2016 -0500 @@ -53,10 +53,18 @@ cp $dir/circos/* $outputDir/circos/ CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" +USECIRCOS="no" +if [ -d "$CIRCOSDIR" ]; then + USECIRCOS="yes" +fi sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf for sample in $samples; do #output the samples to a file and create the circos plots with the R script output echo " $sample" >> $outputFile + if [[ "$USECIRCOS" == "no" ]]; then + continue + fi + circos_file="$outputDir/${sample}_VJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ @@ -119,21 +127,23 @@ #circos -echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile -for sample in $samples; do - echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile - if [[ "$useD" == "true" ]] ; then - echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile - fi - echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile - if [[ "$useD" == "true" ]] ; then - echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile - fi - echo "<center></table></div>" >> $outputFile - count=$((count+1)) -done -echo "</div></div>" >> $outputFile +if [[ "$USECIRCOS" == "no" ]]; then + echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile + for sample in $samples; do + echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + fi + echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + fi + echo "<center></table></div>" >> $outputFile + count=$((count+1)) + done + echo "</div></div>" >> $outputFile +fi #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"