Mercurial > repos > mheinzl > fsd
comparison fsd.xml @ 45:6651e76baca1 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
author | mheinzl |
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date | Tue, 27 Aug 2019 07:36:53 -0400 |
parents | a76af7fd9fca |
children | 901827154779 |
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44:a76af7fd9fca | 45:6651e76baca1 |
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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="FSD" version="1.0.5"> | 3 <tool id="fsd" name="FSD" version="1.0.6"> |
4 <description>: Family Size Distribution of duplex sequencing 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="1.4.0">matplotlib</requirement> | 7 <requirement type="package" version="1.4.0">matplotlib</requirement> |
8 </requirements> | 8 </requirements> |
9 | 9 |
10 <command> | 10 <command> |
11 python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}' | 11 python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}' |
12 --inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}' | 12 --inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}' |
13 --inputFile4 '${file4}' --inputName4 '${file4.name}' $log_axis --output_pdf $output_pdf --output_tabular $output_tabular | 13 --inputFile4 '${file4}' --inputName4 '${file4.name}' $log_axis $rel_freq --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="log_axis" type="boolean" label="log scale for y axis?" truevalue="" falsevalue="--log_axis" checked="False" help="Transform y axis in log scale."/> | 20 <param name="log_axis" type="boolean" label="log scale for y axis?" truevalue="" falsevalue="--log_axis" checked="False" help="Transform y axis in log scale."/> |
21 | 21 <param name="rel_freq" type="boolean" label="relative frequency?" truevalue="" falsevalue="--rel_freq" checked="False" help="If True, the relative frequencies instead of the absolute values are displayed in the plots."/> |
22 </inputs> | 22 </inputs> |
23 <outputs> | 23 <outputs> |
24 <data name="output_pdf" format="pdf" /> | 24 <data name="output_pdf" format="pdf" /> |
25 <data name="output_tabular" format="tabular"/> | 25 <data name="output_tabular" format="tabular"/> |
26 </outputs> | 26 </outputs> |