Mercurial > repos > megan-shortridge > degenerateprimerremoval_fastq

annotate cut_degen.xml @ 0:716cdcccc919 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
author megan-shortridge
date Tue, 15 Sep 2015 14:14:41 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
1 <tool id="cut_degen" name="Cut degenerate primers from dataset (for Fastq)" version="0.1.0">
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
2 <description> Degenerate primer removal tool for Fastq files</description>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
3 <requirements>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
4 <requirement type = "package" version = "1.9">numpy</requirement>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
5 <requirement type = "package" version = "1.65">biopython</requirement>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
6 </requirements>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
7 <stdio>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
8 <exit_code range="1:" />
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
9 </stdio>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
10
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
11 <command interpreter="python">cut_degen.py $input1 $input2 $input3 $input4 $input5 $input6
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
12 </command>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
13 <inputs>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
14 <param name="input1" type="data" label="Input Fastq file" help="Please add a valid Fastq file!" format="fastq"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
15 <param name="input2" type="text" label="Input adaptor" help="This will work also with degenerate adaptors. Type the adaptor here..." size="4x25" area="true"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
16 <param name="input3" type="select" label="Keep reads without adaptor?" help="This is a True/False option, if True, reads that lack the adaptor will be kept. If false, they will be deleted from the dataset.">
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
17 <option value="True">True</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
18 <option value="False">False</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
19 </param>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
20 <param name="input4" type="select" label = "Remove adaptors?" help="This is True/False option, if True, removes adaptors from sequences. If false, keeps the adaptors in the sequences.">
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
21 <option value="True">True</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
22 <option value="False">False</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
23 </param>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
24 <param name="input5" type="select" multiple="False" label="5' or 3' end" help="Enter '5' to remove the primer from the 5' end, and enter '3' to remove the primer from the 3' end">
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
25 <option value="5">5</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
26 <option value="3">3</option>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
27 </param>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
28 <param name="input6" type="text" label="Adaptor name" help="Enter an identifier for your adaptor to be recorded in the output .txt file" size="4x25" area="true">
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
29 </param>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
30 </inputs>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
31 <outputs>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
32 <data name="output1" format="text" from_work_dir="output.txt" label="Degenerate adaptor removal on ${input1.name}(REPORT)"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
33 <data name="output2" format="fastq" from_work_dir="output.fastq" label="Degenerate adaptor removal on ${input1.name}(READS)"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
34 </outputs>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
35 <tests>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
36 <test>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
37 <param name="input1" value="test.fastq"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
38 <param name="input2" value="ACCTGCCTGCCG"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
39 <param name="input3" value="True"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
40 <param name="input4" value="True"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
41 <param name="input5" value="5"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
42 <param name="input6" value="UniA"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
43 <output name="output1" file="output.txt"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
44 <output name="output2" file="output.fastq"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
45 </test>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
46 <test>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
47 <param name="input1" value="test3prime.fastq"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
48 <param name="input2" value="GCTCGGTGGCGT"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
49 <param name="input3" value="True"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
50 <param name="input4" value="True"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
51 <param name="input5" value="3"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
52 <param name="input6" value="UniB"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
53 <output name="output1" file="output2.txt"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
54 <output name="output2" file="output2.fastq"/>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
55 </test>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
56 </tests>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
57 <help>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
58 This program takes Fastq files and removes a given degenerate primer sequence. There are a few arguments that you can put in:
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
59 1) You can check whether or not to keep reads that do not have the adaptor in it.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
60 2) You can check whether or not to remove the adaptor sequences from your reads.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
61 3) You can choose whether to cut adaptors from the 5', or 3' end of the molecules.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
62 4) You can add an identifier for the adaptor which will show up in the output text file.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
63
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
64 </help>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
65 <citations>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
66 <citation type="doi">10.1093/bioinformatics/btp163</citation>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
67 </citations>
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
68 </tool>