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comparison fsd_regions.xml @ 1:9ce2b4089c1b draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
author mheinzl
date Tue, 15 May 2018 13:50:29 -0400
parents b82fdb006304
children 2631864873d7
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0:b82fdb006304 1:9ce2b4089c1b
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:" version="0.0.1"> 2 <tool id="fsd_regions" name="Duplex Sequencing Analysis:" version="0.0.2">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="1.4">matplotlib</requirement> 5 <requirement type="package" version="1.4">matplotlib</requirement>
6 </requirements> 6 </requirements>
7 <description>Family size distribution (FSD) of aligned tags to reference genome</description> 7 <description>Family size distribution (FSD) of aligned tags to reference genome</description>
8 <command> 8 <command>
9 python2 $__tool_directory__/fsd_regions.py --inputFile "$file1" --inputName1 "$file1.name" --ref_genome "$file2" --sep $separator --output_csv $output_csv --output_pdf $output_pdf 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
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 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=","/> 14 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
34 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab | 34 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |
35 +-----+----------------------------+----+ 35 +-----+----------------------------+----+
36 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab | 36 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
37 +-----+----------------------------+----+ 37 +-----+----------------------------+----+
38 38
39 In addition, a TXT file with the regions and all tags that were aligned to the reference genome is required. This file can obtained from a different tool. 39
40 In addition, a TXT file with the regions and all tags that were aligned to the reference genome is required. This file can obtained from a different tool.
40 41
41 +-----------+------------------------------+ 42 +-----------+------------------------------+
42 | 87_636 | AAATCAAAGTATGAATGAAGTTGCCT | 43 | 87_636 | AAATCAAAGTATGAATGAAGTTGCCT |
43 +-----------+------------------------------+ 44 +-----------+------------------------------+
44 | 87_636 | AAATTCATAGCATTAATTTCAACGGG | 45 | 87_636 | AAATTCATAGCATTAATTTCAACGGG |