| Next changeset 1:b7d7ae3963aa (2017-01-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede |
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added:
TagPileup.jar tag_pileup_frequency.xml test-data/input.bam test-data/input.bed test-data/input2_input1_read1_anti.tabular test-data/input2_input1_read1_sense.tabular test-data/output1.tabular |
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| diff -r 000000000000 -r fa82c3c9ced3 TagPileup.jar |
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| Binary file TagPileup.jar has changed |
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| diff -r 000000000000 -r fa82c3c9ced3 tag_pileup_frequency.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tag_pileup_frequency.xml Tue May 17 14:15:39 2016 -0400 |
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| @@ -0,0 +1,114 @@ +<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.0"> + <description></description> + <requirements> + <requirement type="package" version="8.0.45">java-jdk</requirement> + </requirements> + <command> + <![CDATA[ + mkdir -p output && + ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" && + java -jar $__tool_directory__/TagPileup.jar + -b "$input1" + -i "${input1}.bai" + -c "$input2" + -s $tag_shift + -n $bin_size + -e $tags_equal + -r $reads + -p $proper_pe + -a $combine_strands + -t "\${GALAXY_SLOTS:-4}" + -w $composite_smoothing_window + -m "true" + -x "$output1" + -h $output_heatmap + #if str($output_heatmap) == "true": + -o output + #end if + 1>/dev/null + ]]> + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM file" /> + <param name="input2" type="data" format="bed" label="Bed file" /> + <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> + <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> + <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> + <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> + <option value="0" selected="True">Read1</option> + <option value="1">Read2</option> + <option value="2">combined</option> + </param> + <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> + <param name="combine_strands" type="select" label="Combine strands?"> + <option value="0" selected="True">No</option> + <option value="1">Yes</option> + </param> + <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> + <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> + </inputs> + <outputs> + <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="tabular" visible="false" /> + <filter>output_heatmap == true</filter> + </collection> + <data name="output1" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input1" value="input.bam" ftype="bam"/> + <param name="input2" value="input.bed" ftype="bed"/> + <param name="tag_shift" value="0" /> + <param name="bin_size" value="1" /> + <param name="tags_equal" value="false" /> + <param name="reads" value="0" /> + <param name="proper_pe" value="false" /> + <param name="combine_strands" value="0" /> + <param name="composite_smoothing_window" value="0" /> + <param name="output_heatmap" value="true" /> + <output name="output1" file="output1.tabular" ftype="tabular"/> + <output_collection name="heatmaps" type="list"> + <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> + <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> + </output_collection> + </test> + </tests> + <help> + +**What it does** + +Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file. + +----- + +**Options** + +**Global transformations** + + - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs. + - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows. + - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons. + +**Read parameters** + + - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files). + - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files). + - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined). + +**Run parameters** + + - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies. + - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot. + + </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> |
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| diff -r 000000000000 -r fa82c3c9ced3 test-data/input.bam |
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| Binary file test-data/input.bam has changed |
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| diff -r 000000000000 -r fa82c3c9ced3 test-data/input.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.bed Tue May 17 14:15:39 2016 -0400 |
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| @@ -0,0 +1,41 @@ +chr17 958782 958824 chr17_951114_951309_1:0:0_1:0:0_d50af/2 37 + +chr17 1820041 1820100 chr17_1810548_1810721_1:0:0_0:0:0_519fb/1 37 - +chr17 1849174 1849232 chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1 37 + +chr17 2778100 2778159 chr17_2768150_2768389_2:0:0_0:0:0_d422b/1 37 - +chr17 3205460 3205518 chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1 37 - +chr17 4509384 4509441 chr17_4498414_4498642_2:0:0_1:1:0_f20f8/2 37 + +chr17 9677386 9677444 chr17_9676629_9676795_2:0:0_2:0:0_e997/2 37 + +chr17 10089099 10089157 chr17_10088345_10088511_1:0:0_0:0:0_3a7a2/2 37 + +chr17 12974352 12974399 chr17_51669566_51669767_1:0:0_4:0:0_4fa93/1 23 + +chr17 13430901 13430960 chr17_13429910_13430116_0:0:0_1:1:0_7c74f/2 37 + +chr17 15885434 15885477 chr17_15882376_15882562_3:0:0_1:0:0_8ca48/2 37 + +chr17 20624853 20624912 chr17_20622248_20622418_1:0:0_1:0:0_9f20f/1 37 - +chr17 27071126 27071171 chr17_75470822_75470987_3:0:0_2:0:0_4c20e/1 23 - +chr17 27913463 27913508 chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2 25 - +chr17 34920830 34920869 chr17_33286571_33286762_2:0:0_3:0:0_dc02a/1 25 + +chr17 39322684 39322742 chr17_39321131_39321340_1:0:0_1:0:0_db376/2 37 - +chr17 39810522 39810581 chr17_39810082_39810271_0:0:0_0:0:0_7eb08/2 37 + +chr17 39810524 39810583 chr17_39809904_39810133_1:0:0_0:0:0_8c2b/1 37 - +chr17 39960509 39960568 chr17_39959909_39960118_2:0:0_0:0:0_36d84/2 37 - +chr17 43542321 43542379 chr17_43542841_43543044_0:0:0_1:0:0_bda98/1 37 - +chr17 45800655 45800713 chr17_45803004_45803206_2:0:0_0:0:2_41429/1 37 + +chr17 46313026 46313081 chr17_46315776_46315986_1:0:0_0:0:0_e4beb/2 23 + +chr17 47124773 47124830 chr17_47127410_47127618_0:0:0_3:0:0_768f2/1 37 - +chr17 48697937 48697995 chr17_48708043_48708274_1:0:0_1:0:0_1a6/1 37 - +chr17 48697939 48697997 chr17_48708227_48708422_1:0:0_1:0:0_d70c1/2 37 + +chr17 52847681 52847739 chr17_52851082_52851314_1:0:0_1:0:0_6a280/2 37 - +chr17 54474562 54474618 chr17_54477683_54477878_2:0:0_1:0:0_c9f4/1 37 - +chr17 56652426 56652468 chr17_56655628_56655799_1:0:0_1:0:0_28a86/2 37 - +chr17 60951987 60952045 chr17_60960117_60960339_0:1:0_1:0:0_ea16c/2 37 + +chr17 61271205 61271247 chr17_61279152_61279329_1:0:0_1:0:0_477ec/2 37 - +chr17 64901295 64901353 chr17_64907182_64907353_0:0:0_1:0:0_188c2/1 37 - +chr17 64901313 64901371 chr17_64907182_64907371_0:0:0_1:0:0_50fa5/2 37 - +chr17 65065434 65065475 chr17_65071347_65071553_0:0:0_1:0:0_5e8bb/2 37 - +chr17 66772270 66772328 chr17_66777686_66777888_1:0:0_1:0:0_fcea/2 37 - +chr17 68614271 68614328 chr17_68621038_68621213_0:0:0_1:1:0_3ebaf/2 37 - +chr17 69072334 69072383 chr17_1119124_1119366_1:0:0_1:0:0_736b9/1 25 + +chr17 74122686 74122743 chr17_74128589_74128844_1:0:0_1:0:0_b61d8/2 37 + +chr17 76184542 76184601 chr17_76191086_76191297_0:0:0_2:0:0_5f28c/1 37 + +chr17 76518424 76518474 chr17_76526501_76526684_2:0:0_0:0:0_95fe3/2 25 + +chr17 76518826 76518878 chr17_76524679_76524888_0:0:0_0:0:0_8f754/1 37 - +chr17 76941019 76941064 chr17_55336589_55336803_2:0:0_5:0:0_4a6cb/1 23 + |
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| diff -r 000000000000 -r fa82c3c9ced3 test-data/input2_input1_read1_anti.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2_input1_read1_anti.tabular Tue May 17 14:15:39 2016 -0400 |
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| diff -r 000000000000 -r fa82c3c9ced3 test-data/input2_input1_read1_sense.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2_input1_read1_sense.tabular Tue May 17 14:15:39 2016 -0400 |
| b |
| @@ -0,0 +1,15 @@ +YORF NAME 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 +chr17_951114_951309_1:0:0_1:0:0_d50af/2 chr17_951114_951309_1:0:0_1:0:0_d50af/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_1810548_1810721_1:0:0_0:0:0_519fb/1 chr17_1810548_1810721_1:0:0_0:0:0_519fb/1 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1 chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_2768150_2768389_2:0:0_0:0:0_d422b/1 chr17_2768150_2768389_2:0:0_0:0:0_d422b/1 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1 chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_4498414_4498642_2:0:0_1:1:0_f20f8/2 chr17_4498414_4498642_2:0:0_1:1:0_f20f8/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_9676629_9676795_2:0:0_2:0:0_e997/2 chr17_9676629_9676795_2:0:0_2:0:0_e997/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_10088345_10088511_1:0:0_0:0:0_3a7a2/2 chr17_10088345_10088511_1:0:0_0:0:0_3a7a2/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_51669566_51669767_1:0:0_4:0:0_4fa93/1 chr17_51669566_51669767_1:0:0_4:0:0_4fa93/1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_13429910_13430116_0:0:0_1:1:0_7c74f/2 chr17_13429910_13430116_0:0:0_1:1:0_7c74f/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_15882376_15882562_3:0:0_1:0:0_8ca48/2 chr17_15882376_15882562_3:0:0_1:0:0_8ca48/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_20622248_20622418_1:0:0_1:0:0_9f20f/1 chr17_20622248_20622418_1:0:0_1:0:0_9f20f/1 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_75470822_75470987_3:0:0_2:0:0_4c20e/1 chr17_75470822_75470987_3:0:0_2:0:0_4c20e/1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2 chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 |
| b |
| diff -r 000000000000 -r fa82c3c9ced3 test-data/output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tabular Tue May 17 14:15:39 2016 -0400 |
| b |
| @@ -0,0 +1,3 @@ + -28.0 -27.0 -26.0 -25.0 -24.0 -23.0 -22.0 -21.0 -20.0 -19.0 -18.0 -17.0 -16.0 -15.0 -14.0 -13.0 -12.0 -11.0 -10.0 -9.0 -8.0 -7.0 -6.0 -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0 +dataset_2_dataset_1_read1_sense.tabular 0.3170731707317073 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +dataset_2_dataset_1_read1_anti.tabular 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.024390243902439025 0.0 0.0 |