Mercurial > repos > devteam > fasta_compute_length

annotate fasta_compute_length.xml @ 2:de2db1bdfbf8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:13:18 -0500
parents d8cc2c8eef14
children 2051602a5f97
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.1">
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
2 <description></description>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
3 <command interpreter="python">fasta_compute_length.py $input $output $keep_first $keep_first_word</command>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
4 <inputs>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
5 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
6 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
7 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
8 selected="false" label="Strip fasta description from header?"
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
9 help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
10
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
11 </inputs>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
12 <outputs>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
13 <data name="output" format="tabular"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
14 </outputs>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
15 <tests>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
16 <test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
17 <param name="input" value="454.fasta" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
18 <param name="keep_first" value="0"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
19 <param name="keep_first_word" value="id_and_desc" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
20 <output name="output" file="fasta_tool_compute_length_1.out" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
21 </test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
22
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
23 <test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
24 <param name="input" value="extract_genomic_dna_out1.fasta" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
25 <param name="keep_first" value="0"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
26 <param name="keep_first_word" value="id_and_desc" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
27 <output name="output" file="fasta_tool_compute_length_2.out" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
28 </test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
29
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
30 <test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
31 <param name="input" value="454.fasta" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
32 <param name="keep_first" value="14"/>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
33 <param name="keep_first_word" value="id_and_desc" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
34 <output name="output" file="fasta_tool_compute_length_3.out" />
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
35 </test>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
36 </tests>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
37 <help>
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
38
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
39 **What it does**
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
40
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
41 This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
42
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
43 -----
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
44
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
45 **Example**
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
46
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
47 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
48
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
49 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
50 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
51 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
52 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
53 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
54
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
55 Running this tool while setting **How many characters to keep?** to **14** will produce this::
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
56
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
57 EYKX4VC02EQLO5 108
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
58 EYKX4VC02D4GS2 60
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
59
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
60 However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
61
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
62 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
63 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
64 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
65 &gt;EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
66 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
67
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
68 Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
69
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
70 EYKX4VC02EQLO5 108
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
71 EYKX4VC 60
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
72
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
73
2
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
74 </help>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
75 <citations>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
76 <citation type="doi">10.1093/bioinformatics/btq281</citation>
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
77 </citations>
1
d8cc2c8eef14 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
78 </tool>