annotate fsd_regions.xml @ 13:63432e6f6a61 draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit edbe0509294e5c23c26cdae659ce5cf3ff69c363
author mheinzl
date Fri, 07 Dec 2018 07:23:07 -0500
parents fa3ff1c5280d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
10
04c544617b44 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 82b53a26581a2296ad272bbba1e80934864dfa58-dirty
mheinzl
parents: 9
diff changeset
2 <tool id="fsd_regions" name="FSD regions" version="1.0.1">
04c544617b44 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 82b53a26581a2296ad272bbba1e80934864dfa58-dirty
mheinzl
parents: 9
diff changeset
3 <description>:Family size distribution (FSD) of user-specified regions in the reference genome</description>
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
4 <requirements>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
5 <requirement type="package" version="2.7">python</requirement>
4
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
6 <requirement type="package" version="1.4.0">matplotlib</requirement>
12
fa3ff1c5280d planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 5efe7fe08c0603254e1eeafdbc0043e8d94a6c01
mheinzl
parents: 10
diff changeset
7 <requirement type="package" version="0.15">pysam</requirement>
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
8 </requirements>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
9 <command>
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
10 python2 '$__tool_directory__/fsd_regions.py' --inputFile '$file1' --inputName1 '$file1.name' --bamFile '$file2' --rangesFile '$file3' --output_pdf $output_pdf --output_tabular $output_tabular
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
11 </command>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
12 <inputs>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
13 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags of whole dataset" optional="false" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family."/>
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
14 <param name="file2" type="data" format="bam" label="Dataset 2: BAM file of aligned reads." help="Input in BAM format with the reads that were aligned to the reference genome."/>
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
15 <param name="file3" type="data" format="bed" label="Dataset 3: BED file with chromsome, start and stop positions of regions." optional="true" help="BED file with start and stop positions of regions."/>
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
16 </inputs>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
17 <outputs>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
18 <data name="output_pdf" format="pdf" />
4
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
19 <data name="output_tabular" format="tabular"/>
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
20 </outputs>
4
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
21 <tests>
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
22 <test>
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
23 <param name="file1" value="fsd_reg.tab"/>
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
24 <param name="file2" value="fsd_reg.bam"/>
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
25 <param name="file3" value="fsd_reg_ranges.bed"/>
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
26 <output name="output_pdf" file="fsd_reg_output.pdf" lines_diff="136"/>
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
27 <output name="output_tabular" file="fsd_reg_output.tab"/>
4
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
28 </test>
b202c97deabe planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 3
diff changeset
29 </tests>
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
30 <help> <![CDATA[
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
31
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
32 **What it does**
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
33
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
34 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.
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
35
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
36
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
37 **Input**
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
38
10
04c544617b44 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 82b53a26581a2296ad272bbba1e80934864dfa58-dirty
mheinzl
parents: 9
diff changeset
39 **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::
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
40
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
41 1 AAAAAAAAAAAATGTTGGAATCTT ba
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
42 10 AAAAAAAAAAAGGCGGTCCACCCC ab
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
43 28 AAAAAAAAAAATGGTATGGACCGA ab
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
44
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
45 **Dataset 2:** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM".
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
46
10
04c544617b44 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 82b53a26581a2296ad272bbba1e80934864dfa58-dirty
mheinzl
parents: 9
diff changeset
47 **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::
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
48
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
49 ACH_TDII 90 633
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
50 ACH_TDII 659 1140
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
51 ACH_TDII 1144 1561
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
52
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
53 **Output**
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
54
9
eabfdc012d7b planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 31f11c1cb3303d741ee11a25903c3cc42a23f30d
mheinzl
parents: 4
diff changeset
55 The output is a PDF file with the plot and a tabular file with the data of the plot.
0
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
56
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
57
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
58 **About Author**
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
59
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
60 Author: Monika Heinzl
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
61
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
62 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
63
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
64 Contact: monika.heinzl@edumail.at
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
65
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
66 ]]>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
67
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
68 </help>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
69 <citations>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
70 <citation type="bibtex">
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
71 @misc{duplex,
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
72 author = {Heinzl, Monika},
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
73 year = {2018},
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
74 title = {Development of algorithms for the analysis of duplex sequencing data}
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
75 }
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
76 </citation>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
77 </citations>
b82fdb006304 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
78 </tool>