Mercurial > repos > iuc > pe_histogram
changeset 0:2f6c7f82ad4a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 05bab1b3b5838d62307a2d0d1172445b765b7f55
| author | iuc |
|---|---|
| date | Mon, 20 Jun 2016 13:02:17 -0400 |
| parents | |
| children | b1a427b17e9c |
| files | PEHistogram.jar pe_histogram.xml test-data/input.bam test-data/output1.png test-data/output1.tabular test-data/output2.png test-data/output2.tabular |
| diffstat | 7 files changed, 283 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pe_histogram.xml Mon Jun 20 13:02:17 2016 -0400 @@ -0,0 +1,81 @@ +<tool id="pe_histogram" name="Paired-end histogram" version="1.0.0"> + <description>of insert size frequency</description> + <requirements> + <requirement type="package" version="8.0.45">java-jdk</requirement> + </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range=":-1" /> + <exit_code range="1:" /> + <!-- Check stderr in case the return code has not been set --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <command> + <![CDATA[ + ln -s "${input_bam}" "localbam.bam" && + ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && + java -jar $__tool_directory__/PEHistogram.jar + -B "localbam.bam" + -I "localbam.bam.bai" + #if str($lower_limit) != '': + -l $lower_limit + #end if + #if str($upper_limit) != '': + -u $upper_limit + #end if + -p "$output1" + -t "$output2" 1>/dev/null + ]]> + </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/> + <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." /> + </inputs> + <outputs> + <data name="output1" format="png" /> + <data name="output2" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="input.bam" ftype="bam" /> + <output name="output1" file="output1.png" ftype="png" compare="sim_size" /> + <output name="output2" file="output1.tabular" ftype="tabular" compare="contains" /> + </test> + <test> + <param name="input_bam" value="input.bam" ftype="bam" /> + <param name="lower_limit" value="200" /> + <param name="upper_limit" value="300" /> + <output name="output1" file="output2.png" ftype="png" compare="sim_size" /> + <output name="output2" file="output2.tabular" ftype="tabular" compare="contains" /> + </test> + </tests> + <help> + +**What it does** + +Produces an insert size histogram and basic statistics for a paired-end BAM file. Two outputs are produced: + +- a png image consisting of the histogram of the insert size frequency +- a tabular file containing the alignment statistics + +----- + +**Options** + +* **Lower bp limit** - the lower bp limit on insert size for calculating the histogram. +* **Upper bp limit** - the upper bp limit on insert size for calculating the histogram. + + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {Lai, William}, + title = {None}, + year = {None}, + eprint = {None}, + url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tabular Mon Jun 20 13:02:17 2016 -0400 @@ -0,0 +1,100 @@ +# Size (bp) Frequency +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 +14 0.0 +15 0.0 +16 0.0 +17 0.0 +18 0.0 +19 0.0 +20 0.0 +21 0.0 +22 0.0 +23 0.0 +24 0.0 +25 0.0 +26 0.0 +27 0.0 +28 0.0 +29 0.0 +30 0.0 +31 0.0 +32 0.0 +33 0.0 +34 0.0 +35 0.0 +36 0.0 +37 0.0 +38 0.0 +39 0.0 +40 0.0 +41 0.0 +42 0.0 +43 0.0 +44 0.0 +45 0.0 +46 0.0 +47 0.0 +48 0.0 +49 0.0 +50 0.0 +51 0.0 +52 0.0 +53 0.0 +54 0.0 +55 0.0 +56 0.0 +57 0.0 +58 0.0 +59 0.0 +60 0.0 +61 0.0 +62 0.0 +63 0.0 +64 0.0 +65 0.0 +66 0.0 +67 0.0 +68 0.0 +69 0.0 +70 0.0 +71 0.0 +72 0.0 +73 0.0 +74 0.0 +75 0.0 +76 0.0 +77 0.0 +78 0.0 +79 0.0 +80 0.0 +81 0.0 +82 0.0 +83 0.0 +84 0.0 +85 0.0 +86 0.0 +87 0.0 +88 0.0 +89 0.0 +90 0.0 +91 0.0 +92 0.0 +93 0.0 +94 0.0 +95 0.0 +96 0.0 +97 0.0 +98 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.tabular Mon Jun 20 13:02:17 2016 -0400 @@ -0,0 +1,102 @@ +# Size (bp) Frequency +200 0.0 +201 0.0 +202 1.0 +203 0.0 +204 1.0 +205 0.0 +206 0.0 +207 0.0 +208 0.0 +209 0.0 +210 1.0 +211 1.0 +212 1.0 +213 0.0 +214 0.0 +215 0.0 +216 1.0 +217 0.0 +218 0.0 +219 0.0 +220 0.0 +221 1.0 +222 0.0 +223 0.0 +224 0.0 +225 0.0 +226 0.0 +227 0.0 +228 0.0 +229 0.0 +230 0.0 +231 0.0 +232 0.0 +233 0.0 +234 0.0 +235 0.0 +236 0.0 +237 0.0 +238 0.0 +239 1.0 +240 1.0 +241 1.0 +242 0.0 +243 0.0 +244 0.0 +245 0.0 +246 0.0 +247 0.0 +248 0.0 +249 1.0 +250 0.0 +251 0.0 +252 0.0 +253 0.0 +254 0.0 +255 0.0 +256 0.0 +257 0.0 +258 0.0 +259 0.0 +260 0.0 +261 0.0 +262 0.0 +263 0.0 +264 0.0 +265 0.0 +266 0.0 +267 0.0 +268 0.0 +269 0.0 +270 0.0 +271 0.0 +272 0.0 +273 0.0 +274 0.0 +275 0.0 +276 0.0 +277 0.0 +278 0.0 +279 0.0 +280 0.0 +281 0.0 +282 0.0 +283 0.0 +284 0.0 +285 0.0 +286 0.0 +287 0.0 +288 0.0 +289 0.0 +290 0.0 +291 0.0 +292 0.0 +293 0.0 +294 0.0 +295 0.0 +296 0.0 +297 0.0 +298 0.0 +299 0.0 +300 0.0