Mercurial > repos > mheinzl > fsd_regions
comparison fsd_regions.xml @ 4:b202c97deabe draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author | mheinzl |
---|---|
date | Mon, 08 Oct 2018 05:53:50 -0400 |
parents | 85d870b8ae92 |
children | eabfdc012d7b |
comparison
equal
deleted
inserted
replaced
3:85d870b8ae92 | 4:b202c97deabe |
---|---|
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="0.0.4"> | 2 <tool id="fsd_regions" name="Duplex Sequencing Analysis: fsd_regions" version="1.0.0"> |
3 <description>Family size distribution (FSD) of user-specified regions in the reference genome</description> | |
3 <requirements> | 4 <requirements> |
4 <requirement type="package" version="2.7">python</requirement> | 5 <requirement type="package" version="2.7">python</requirement> |
5 <requirement type="package" version="1.4">matplotlib</requirement> | 6 <requirement type="package" version="1.4.0">matplotlib</requirement> |
6 </requirements> | 7 </requirements> |
7 <description>Family size distribution (FSD) of user-specified regions</description> | |
8 <command> | 8 <command> |
9 python2 $__tool_directory__/fsd_regions.py --inputFile "$file1" --inputName1 "$file1.name" --ref_genome "$file2" --sep $separator --output_pdf $output_pdf --output_csv $output_csv | 9 python2 '$__tool_directory__/fsd_regions.py' --inputFile '$file1' --inputName1 '$file1.name' --ref_genome '$file2' --output_pdf $output_pdf --output_tabular $output_tabular |
10 </command> | 10 </command> |
11 <inputs> | 11 <inputs> |
12 <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."/> | 12 <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."/> |
13 <param name="file2" type="data" format="txt" label="Dataset 2: input tags aligned to the reference genome" help="Input in txt format with the regions and the tags, which were aligned to the reference genome."/> | 13 <param name="file2" type="data" format="txt" label="Dataset 2: input tags aligned to the reference genome" help="Input in txt format with the regions in the reference genome and the tags, which were aligned to the reference genome."/> |
14 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/> | |
15 </inputs> | 14 </inputs> |
16 <outputs> | 15 <outputs> |
17 <data name="output_pdf" format="pdf" /> | 16 <data name="output_pdf" format="pdf" /> |
18 <data name="output_csv" format="csv"/> | 17 <data name="output_tabular" format="tabular"/> |
19 </outputs> | 18 </outputs> |
19 <tests> | |
20 <test> | |
21 <param name="file1" value="Test_data.tabular"/> | |
22 <param name="file2" value="Test_data_regions.txt"/> | |
23 <output name="output_pdf" file="output_file.pdf" lines_diff="136"/> | |
24 <output name="output_tabular" file="output_file.tabular"/> | |
25 </test> | |
26 </tests> | |
20 <help> <![CDATA[ | 27 <help> <![CDATA[ |
21 | 28 |
22 **What it does** | 29 **What it does** |
23 | 30 |
24 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. | 31 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. |
47 | 656_1143 | GGGGCAGCCATATTGGCAATTATCAT | | 54 | 656_1143 | GGGGCAGCCATATTGGCAATTATCAT | |
48 +-----------+------------------------------+ | 55 +-----------+------------------------------+ |
49 | 56 |
50 **Output** | 57 **Output** |
51 | 58 |
52 The output is a PDF file with the plot and a CSV with the data of the plot. | 59 The output is a PDF file with the plot and a tabular file with the data of the plot. |
53 | 60 |
54 | 61 |
55 **About Author** | 62 **About Author** |
56 | 63 |
57 Author: Monika Heinzl | 64 Author: Monika Heinzl |