Mercurial > repos > malex > bayesase
comparison drop_reads_that_doNot_overlap_after_BEDtools_intersect.xml @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
author | malex |
---|---|
date | Thu, 14 Jan 2021 21:51:36 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:e979cb57a5d5 |
---|---|
1 <tool id="base_remove_nonoverlapping_reads" name="Remove reads" version="21.1.13"> | |
2 <description>that do not overlap with genic features for BayesASE (using awk)</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command> | |
8 <![CDATA[ | |
9 awk -v OFS=' ' '$4 !="."' '$BEDINT' > '$BED3'; | |
10 awk -v a=0 'BEGIN{print "fqName\tnumber_overlapping_rows\ttotal_number_rows"} {if($4 !=".") a++} END{print "$BEDINT.element_identifier""\t"a"\t"NR }' '$BED3' > $summary | |
11 ]]> | |
12 </command> | |
13 <inputs> | |
14 <param name="BEDINT" type="data" format="tabular" label="Output from Bedtools Intersect Intervals" help="Input BED file made from loj intersection between BED files with location of unique reads and features of interest" /> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="BED3" format="tabular" label="${tool.name} on ${on_string}: Multi-column BED file with overlapping reads" /> | |
18 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: output summary file" /> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="BEDINT" ftype="data" value="align_and_counts_test_data/bedtools_intersect_intervals_BASE_test_data.bed"/> | |
23 <output name="BED3" ftype="data" file="align_and_counts_test_data/drop_nonintersecting_reads_for_BASE.tabular" /> | |
24 </test> | |
25 </tests> | |
26 <help><![CDATA[ | |
27 **Tool Description** | |
28 | |
29 The purpose of this tool is to remove reads from the input BED file that do not intersect with any genic features. | |
30 The input into this tool is generated by the **BedTools Intersect Intervals** and may contain rows where a read does not intersect with any genic features. These rows contain a “.” in the ThickStart column. | |
31 The resulting output BED file contains locations of unique reads that overlap with regions of genic features. | |
32 | |
33 ----------------------------------------------------------------------------------------------- | |
34 | |
35 **Inputs** | |
36 -One input dataset is required. | |
37 | |
38 **BED File [REQUIRED]** | |
39 | |
40 -A BED file resulting from the intersection of a SAM file in BED format and a BED file of genic features. | |
41 This input BED file can be generated with the **BedTools Intersect Intervals** tool. | |
42 | |
43 Example input BED file: | |
44 | |
45 +-------------+---------+---------+---------+---------+------------+------------+ | |
46 | Chrom | Start | End | Name | Score | Strand |ThickStart | | |
47 +=============+=========+=========+=========+=========+============+============+ | |
48 | X | 2190 | 2245 | X | 1 | 2300 |l(1)G0196 | | |
49 +-------------+---------+---------+---------+---------+------------+------------+ | |
50 | 2R | 1502 | 1834 | 2R | 50 | 1900 | Mapmodulin | | |
51 +-------------+---------+---------+---------+---------+------------+------------+ | |
52 | 2R | 1621 | 1680 | . | -1 |-1 |. | | |
53 +-------------+---------+---------+---------+---------+------------+------------+ | |
54 | |
55 | |
56 **Outputs** | |
57 The tool outputs a BED file containing regions of reads that overlap with locations of genic features interest. | |
58 | |
59 Example output BED file: | |
60 | |
61 +---------------+---------+---------+---------+---------+------------+------------+ | |
62 | Chrom | Start | End | Name | Score | Strand |ThickStart | | |
63 +===============+=========+=========+=========+=========+============+============+ | |
64 | X | 2190 | 2245 | X | 1 | 2300 |l(1)G0196 | | |
65 +---------------+---------+---------+---------+---------+------------+------------+ | |
66 | 2R | 1502 | 1834 | 2R | 50 |19000 |Mapmodulin | | |
67 +---------------+---------+---------+---------+---------+------------+------------+ | |
68 ]]></help> | |
69 <citations> | |
70 <citation type="bibtex">@ARTICLE{Miller20BASE, | |
71 author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre}, | |
72 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, | |
73 journal = {????}, | |
74 year = {submitted for publication} | |
75 }</citation> | |
76 </citations> | |
77 </tool> |