Mercurial > repos > mheinzl > fsd
comparison fsd.xml @ 16:6bd9ef49d013 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author | mheinzl |
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date | Mon, 08 Oct 2018 05:50:18 -0400 |
parents | 32921a67437b |
children | 2e517a54eedc |
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15:32921a67437b | 16:6bd9ef49d013 |
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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}, |