Mercurial > repos > mheinzl > fsd_regions

comparison fsd_regions.xml @ 10:04c544617b44 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 82b53a26581a2296ad272bbba1e80934864dfa58-dirty
author mheinzl
date Mon, 26 Nov 2018 04:42:25 -0500
parents eabfdc012d7b
children fa3ff1c5280d
comparison
equal deleted inserted replaced
9:eabfdc012d7b 10:04c544617b44
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="fsd_regions" name="Duplex Sequencing Analysis: fsd_regions" version="1.0.1"> 2 <tool id="fsd_regions" name="FSD regions" version="1.0.1">
3 <description>Family size distribution (FSD) of user-specified regions in the reference genome</description> 3 <description>:Family size distribution (FSD) of user-specified regions in the reference genome</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.7">python</requirement> 5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package" version="1.4.0">matplotlib</requirement> 6 <requirement type="package" version="1.4.0">matplotlib</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
33 This tool will create a distribution of family sizes of all tags, which were aligned to the reference genome. The distribution is separated after the regions of the reference genome. 33 This tool will create a distribution of family sizes of all tags, which were aligned to the reference genome. The distribution is separated after the regions of the reference genome.
34 34
35 35
36 **Input** 36 **Input**
37 37
38 **Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. 38 **Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands::
39 39
40 1 AAAAAAAAAAAATGTTGGAATCTT ba 40 1 AAAAAAAAAAAATGTTGGAATCTT ba
41 10 AAAAAAAAAAAGGCGGTCCACCCC ab 41 10 AAAAAAAAAAAGGCGGTCCACCCC ab
42 28 AAAAAAAAAAATGGTATGGACCGA ab 42 28 AAAAAAAAAAATGGTATGGACCGA ab
43 43
44 **Dataset 2:** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM". 44 **Dataset 2:** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM".
45 45
46 **Dataset 3 (optional):** BED file with start and stop positions of the regions. If it is not provided, then all aligned reads of the BAM file are used in the distribution of family sizes. 46 **Dataset 3 (optional):** BED file with start and stop positions of the regions. If it is not provided, then all aligned reads of the BAM file are used in the distribution of family sizes::
47 47
48 ACH_TDII 90 633 48 ACH_TDII 90 633
49 ACH_TDII 659 1140 49 ACH_TDII 659 1140
50 ACH_TDII 1144 1561 50 ACH_TDII 1144 1561
51 51