Mercurial > repos > iuc > tag_pileup_frequency
comparison tag_pileup_frequency.xml @ 0:fa82c3c9ced3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author | iuc |
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date | Tue, 17 May 2016 14:15:39 -0400 |
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children | b7d7ae3963aa |
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1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.0"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="8.0.45">java-jdk</requirement> | |
5 </requirements> | |
6 <command> | |
7 <![CDATA[ | |
8 mkdir -p output && | |
9 ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" && | |
10 java -jar $__tool_directory__/TagPileup.jar | |
11 -b "$input1" | |
12 -i "${input1}.bai" | |
13 -c "$input2" | |
14 -s $tag_shift | |
15 -n $bin_size | |
16 -e $tags_equal | |
17 -r $reads | |
18 -p $proper_pe | |
19 -a $combine_strands | |
20 -t "\${GALAXY_SLOTS:-4}" | |
21 -w $composite_smoothing_window | |
22 -m "true" | |
23 -x "$output1" | |
24 -h $output_heatmap | |
25 #if str($output_heatmap) == "true": | |
26 -o output | |
27 #end if | |
28 1>/dev/null | |
29 ]]> | |
30 </command> | |
31 <inputs> | |
32 <param name="input1" type="data" format="bam" label="BAM file" /> | |
33 <param name="input2" type="data" format="bed" label="Bed file" /> | |
34 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> | |
35 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> | |
36 <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> | |
37 <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> | |
38 <option value="0" selected="True">Read1</option> | |
39 <option value="1">Read2</option> | |
40 <option value="2">combined</option> | |
41 </param> | |
42 <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> | |
43 <param name="combine_strands" type="select" label="Combine strands?"> | |
44 <option value="0" selected="True">No</option> | |
45 <option value="1">Yes</option> | |
46 </param> | |
47 <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> | |
48 <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> | |
49 </inputs> | |
50 <outputs> | |
51 <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}"> | |
52 <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="tabular" visible="false" /> | |
53 <filter>output_heatmap == true</filter> | |
54 </collection> | |
55 <data name="output1" format="tabular"/> | |
56 </outputs> | |
57 <tests> | |
58 <test> | |
59 <param name="input1" value="input.bam" ftype="bam"/> | |
60 <param name="input2" value="input.bed" ftype="bed"/> | |
61 <param name="tag_shift" value="0" /> | |
62 <param name="bin_size" value="1" /> | |
63 <param name="tags_equal" value="false" /> | |
64 <param name="reads" value="0" /> | |
65 <param name="proper_pe" value="false" /> | |
66 <param name="combine_strands" value="0" /> | |
67 <param name="composite_smoothing_window" value="0" /> | |
68 <param name="output_heatmap" value="true" /> | |
69 <output name="output1" file="output1.tabular" ftype="tabular"/> | |
70 <output_collection name="heatmaps" type="list"> | |
71 <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> | |
72 <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> | |
73 </output_collection> | |
74 </test> | |
75 </tests> | |
76 <help> | |
77 | |
78 **What it does** | |
79 | |
80 Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file. | |
81 | |
82 ----- | |
83 | |
84 **Options** | |
85 | |
86 **Global transformations** | |
87 | |
88 - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs. | |
89 - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows. | |
90 - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons. | |
91 | |
92 **Read parameters** | |
93 | |
94 - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files). | |
95 - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files). | |
96 - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined). | |
97 | |
98 **Run parameters** | |
99 | |
100 - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies. | |
101 - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot. | |
102 | |
103 </help> | |
104 <citations> | |
105 <citation type="bibtex"> | |
106 @unpublished{None, | |
107 author = {Lai, William}, | |
108 title = {None}, | |
109 year = {None}, | |
110 eprint = {None}, | |
111 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} | |
112 }</citation> | |
113 </citations> | |
114 </tool> |