Mercurial > repos > erinija > shuffle_sequences

annotate shuffle_sequences.xml @ 0:424506a8adf7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:11:39 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
1 <tool id="shuffle_sequences" name="Shuffle nucleotides in fasta" version="0.1.0">
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
2 <requirements>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
3 <requirement type="package" version="1.2.2">ushuffle</requirement>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
4 </requirements>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
5 <command detect_errors="exit_code" interpreter="sh"><![CDATA[
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
6 shuffle_sequences.sh "$input1" "$input2" "$output1"
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
7 ]]></command>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
8 <inputs>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
9 <param type="data" name="input1" format="fasta" label="From fasta"/>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
10 <param type="integer" name="input2" value="2" label="preserve frequency of k-mers" />
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
11 </inputs>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
12 <outputs>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
13 <data name="output1" format="fasta" />
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
14 </outputs>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
15 <tests>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
16 <test>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
17 <param name="input1" value="seq1000.fasta"/>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
18 <param name="input2" value="2"/>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
19 <output name="output1">
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
20 <assert_contents>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
21 <has_text text=">chr9:42475963-42476182" />
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
22 <has_text text=">chr9:42566360-42566579" />
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
23 <has_n_lines n="2000" />
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
24 </assert_contents>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
25 </output>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
26 </test>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
27 </tests>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
28 <help><![CDATA[
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
29
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
30
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
31 CALL
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
32 sh shuffle_sequences.sh input.fasta k output.fasta
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
33
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
34 INPUT
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
35 input.fasta - input fasta file
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
36 k - 'preserve frequency of k letters (dinucleotide k=2)'
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
37
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
38 OUTPUT
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
39 output.fasta - shuffle fasta file
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
40
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
41 DESCRIPTION
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
42 Wrapper for ushuffle program written by M. Jiang.
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
43 The ushuffle shuffles nucleotides in fasta sequence preserving frequency
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
44 of k-mers, a positional order is changed. By default k=2.
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
45 A sequence in fasta file is shuffled only once. The output fasta
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
46 in the identifier line contains the original sequence; a shuffled sequence
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
47 is output on the second line.
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
48
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
49 REQUIREMENT
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
50 ushuffle installed
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
51 conda install -c bioconda ushuffle
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
52
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
53
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
54 ]]></help>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
55 <citations>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
56 <citation type="bibtex">
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
57 @article{jiang2008ushuffle,
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
58 title={uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
59 author={Jiang, Minghui and Anderson, James and Gillespie, Joel and Mayne, Martin},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
60 journal={BMC bioinformatics},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
61 volume={9},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
62 number={1},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
63 pages={192},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
64 year={2008},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
65 publisher={Springer},
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
66 url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-192}
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
67 }</citation>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
68 </citations>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
69 </tool>
424506a8adf7 "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
70