annotate fsd.xml @ 16:6bd9ef49d013 draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
author mheinzl
date Mon, 08 Oct 2018 05:50:18 -0400
parents 32921a67437b
children 2e517a54eedc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
4
5bae51dc7fa1 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 84c5a0c42a666f70c4328e7ed85523a036d52e17
mheinzl
parents: 3
diff changeset
2 <!-- galaxy version 16.04 -->
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
3 <tool id="fsd" name="FSD" version="1.0.0">
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
4 <description>: Family Size Distribution of duplex sequencing tags</description>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
5 <requirements>
8
7d5c86d59850 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 72152f9651d7b1ecc84052f967d2746813481af6
mheinzl
parents: 7
diff changeset
6 <requirement type="package" version="2.7">python</requirement>
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
7 <requirement type="package" version="1.4.0">matplotlib</requirement>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
8 </requirements>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
9
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
10 <command>
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
11 python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}'
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
12 --inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}'
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
13 --inputFile4 '${file4}' --inputName4 '${file4.name}' --output_pdf $output_pdf --output_tabular $output_tabular
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
14 </command>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
15 <inputs>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
16 <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
17 <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" />
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
18 <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
10
f7136e93604b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
mheinzl
parents: 9
diff changeset
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!"/>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
20 </inputs>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
21 <outputs>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
22 <data name="output_pdf" format="pdf" />
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
23 <data name="output_tabular" format="tabular"/>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
24 </outputs>
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
25 <tests>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
26 <test>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
27 <param name="file1" value="Test_data.tabular"/>
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
28 <param name="file2" value="Test_data2.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
29 <param name="file3" value="Test_data3.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
30 <param name="file4" value="Test_data4.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
31 <output name="output_pdf" file="output_file.pdf" lines_diff="285"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
32 <output name="output_tabular" file="output_file.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
33 </test>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
34 <test>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
35 <param name="file1" value="Test_data.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
36 <param name="file2" value="Test_data2.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
37 <param name="file3" value="Test_data3.tabular"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
38 <output name="output_pdf" file="output_file2.pdf" lines_diff="285"/>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
39 <output name="output_tabular" file="output_file2.tabular"/>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
40 </test>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
41 </tests>
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
42 <help><![CDATA[
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
43
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
44 **What it does**
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
45
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
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.
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
47
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
48 ------
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
49
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
50 **Input**
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
51
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
52 This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands::
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
53
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
54 1 AAAAAAAAAAAATGTTGGAATCTT ba
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
55 10 AAAAAAAAAAAGGCGGTCCACCCC ab
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
56 28 AAAAAAAAAAATGGTATGGACCGA ab
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
57
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
58 **Output**
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
59
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
60 The output is a PDF file with the plot and a tabular file with the data of the plot.
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
61
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
62 **About Author**
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
63
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
64 Author: Monika Heinzl
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
65 Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
66 Contact: monika.heinzl@edumail.at
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
67
16
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
68 ]]>
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents: 15
diff changeset
69 </help>
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
70 <citations>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
71 <citation type="bibtex">
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
72 @misc{duplex,
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
73 author = {Heinzl, Monika},
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
74 year = {2018},
3
648d5df50ca8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 86722bdca280f0bbe6b2a9342734edcb484ca789
mheinzl
parents: 2
diff changeset
75 title = {Development of algorithms for the analysis of duplex sequencing data}
0
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
76 }
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
77 </citation>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
78 </citations>
9736b9d04a0b planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit f674213e798956531c935e7b9eb7f444286d0a5e-dirty
mheinzl
parents:
diff changeset
79 </tool>