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comparison fsd.xml @ 10:f7136e93604b draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
author mheinzl
date Tue, 15 May 2018 13:49:34 -0400
parents 2c5fc522ded4
children b615c7e51f40
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9:2c5fc522ded4 10:f7136e93604b
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:" version="0.0.10"> 3 <tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.11">
4 <description>Family size distribution (FSD) of tags</description> 4 <description>Family size distribution (FSD) of 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">matplotlib</requirement>
8 </requirements> 8 </requirements>
9 9
10 <command> 10 <command>
11 python2 $__tool_directory__/fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_csv $output_csv --output_pdf $output_pdf 11 python2 $__tool_directory__/fsd.py --inputFile1 "$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
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/> 14 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
15 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" /> 15 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
16 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" /> 16 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
17 <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, blanks are not allowed!"/> 17 <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!"/>
18 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/> 18 <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data name="output_pdf" format="pdf" /> 21 <data name="output_pdf" format="pdf" />
22 <data name="output_csv" format="csv"/> 22 <data name="output_csv" format="csv"/>
41 41
42 **Input** 42 **Input**
43 43
44 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. 44 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands.
45 45
46 **!!! Name of the files can have max. 34 charcters, blanks are not allowed !!!** 46 **!!! Name of the files can have max. 34 charcters !!!**
47 47
48 +-----+----------------------------+----+ 48 +-----+----------------------------+----+
49 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba | 49 | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba |
50 +-----+----------------------------+----+ 50 +-----+----------------------------+----+
51 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab | 51 | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab |