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changeset 0:fa82c3c9ced3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author iuc
date Tue, 17 May 2016 14:15:39 -0400
parents
children b7d7ae3963aa
files 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
diffstat 7 files changed, 188 insertions(+), 0 deletions(-) [+]
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Binary file TagPileup.jar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tag_pileup_frequency.xml	Tue May 17 14:15:39 2016 -0400
@@ -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&lt;designation&gt;.*)" 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>
Binary file test-data/input.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.bed	Tue May 17 14:15:39 2016 -0400
@@ -0,0 +1,41 @@
+chr17	958782	958824	chr17_951114_951309_1:0:0_1:0:0_d50af/2	37	+
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+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	+
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+chr17	20624853	20624912	chr17_20622248_20622418_1:0:0_1:0:0_9f20f/1	37	-
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+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	-
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+chr17	52847681	52847739	chr17_52851082_52851314_1:0:0_1:0:0_6a280/2	37	-
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+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	-
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+chr17	64901313	64901371	chr17_64907182_64907371_0:0:0_1:0:0_50fa5/2	37	-
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+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	+
--- /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
@@ -0,0 +1,15 @@
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+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
--- /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
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.tabular	Tue May 17 14:15:39 2016 -0400
@@ -0,0 +1,3 @@
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+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