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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author mheinzl
date Mon, 08 Oct 2018 05:50:18 -0400
parents 32921a67437b
children 2e517a54eedc
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15:32921a67437b 16:6bd9ef49d013
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- galaxy version 16.04 --> 2 <!-- galaxy version 16.04 -->
3 <tool id="fsd" name="Duplex Sequencing Analysis: fsd" version="0.0.16"> 3 <tool id="fsd" name="FSD" version="1.0.0">
4 <description>Family size distribution (FSD) of tags</description> 4 <description>: Family Size Distribution of duplex sequencing tags</description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.7">python</requirement> 6 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package" version="1.4">matplotlib</requirement> 7 <requirement type="package" version="1.4.0">matplotlib</requirement>
8 <requirement type="package" version="0.0.2">duplexanalysis</requirement>
9
10 </requirements> 8 </requirements>
11 9
12 <command> 10 <command>
13 fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_pdf $output_pdf --output_csv $output_csv 11 python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}'
12 --inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}'
13 --inputFile4 '${file4}' --inputName4 '${file4.name}' --output_pdf $output_pdf --output_tabular $output_tabular
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/> 16 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
17 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" /> 17 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
18 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" /> 18 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
19 <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters!"/> 19 <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters!"/>
20 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
21 </inputs> 20 </inputs>
22 <outputs> 21 <outputs>
23 <data name="output_pdf" format="pdf" /> 22 <data name="output_pdf" format="pdf" />
24 <data name="output_csv" format="csv"/> 23 <data name="output_tabular" format="tabular"/>
25 </outputs> 24 </outputs>
26 <!-- <tests> 25 <tests>
27 <test> 26 <test>
28 <param name="file1" value="Test_data.tabular"/> 27 <param name="file1" value="Test_data.tabular"/>
29 <param name="file2" value="None"/> 28 <param name="file2" value="Test_data2.tabular"/>
30 <param name="file3" value="None"/> 29 <param name="file3" value="Test_data3.tabular"/>
31 <param name="file4" value="None"/> 30 <param name="file4" value="Test_data4.tabular"/>
32 <output name="output_pdf" file="output_file.pdf"/> 31 <output name="output_pdf" file="output_file.pdf" lines_diff="285"/>
33 <output name="output_csv" file="output_file.csv"/> 32 <output name="output_tabular" file="output_file.tabular"/>
33 </test>
34 <test>
35 <param name="file1" value="Test_data.tabular"/>
36 <param name="file2" value="Test_data2.tabular"/>
37 <param name="file3" value="Test_data3.tabular"/>
38 <output name="output_pdf" file="output_file2.pdf" lines_diff="285"/>
39 <output name="output_tabular" file="output_file2.tabular"/>
34 </test> 40 </test>
35 </tests> 41 </tests>
36 --> 42 <help><![CDATA[
37 <help> <![CDATA[
38 43
39 **What it does** 44 **What it does**
40 45
41 This tool will create a distribution of family sizes of each tag, which is separated after families tags that have only the forward (ab) strand, the reverse (ba) strand or both strands (ab+ba) of the DCS and a family size distribution without separation is created. If multiple files are provided as input, the family size distribution without separation contains all datasets in one plot and for each dataset a distribution with separation after single ab, ba strands and DCSs is produced. 46 This tool will create a distribution of family sizes of each tag, which is separated after tags that have only the forward (ab) strand, the reverse (ba) strand or both strands (ab+ba) of the DCS and a family size distribution without separation is created.
42 47
48 ------
43 49
44 **Input** 50 **Input**
45 51
46 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. 52 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands::
47 53
48 **!!! Name of the files can have max. 34 charcters !!!** 54 1 AAAAAAAAAAAATGTTGGAATCTT ba
49 55 10 AAAAAAAAAAAGGCGGTCCACCCC ab
50 +-----+----------------------------+----+ 56 28 AAAAAAAAAAATGGTATGGACCGA ab
51 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba | 57
52 +-----+----------------------------+----+
53 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
54 +-----+----------------------------+----+
55 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
56 +-----+----------------------------+----+
57
58
59
60
61
62 **Output** 58 **Output**
63 59
64 The output is a PDF file with the plot and a CSV with the data of the plot. 60 The output is a PDF file with the plot and a tabular file with the data of the plot.
65
66 61
67 **About Author** 62 **About Author**
68 63
69 Author: Monika Heinzl 64 Author: Monika Heinzl
70 65 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
71 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria 66 Contact: monika.heinzl@edumail.at
72
73 Contact: monika.heinzl@edumail.at
74 67
75 ]]> 68 ]]>
76 69 </help>
77 </help>
78 <citations> 70 <citations>
79 <citation type="bibtex"> 71 <citation type="bibtex">
80 @misc{duplex, 72 @misc{duplex,
81 author = {Heinzl, Monika}, 73 author = {Heinzl, Monika},
82 year = {2018}, 74 year = {2018},