Mercurial > repos > devteam > fasta_compute_length

annotate fasta_compute_length.xml @ 5:7d37cfda8e00 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 34a6c9f94a5722bb7d2f887618aafa410a770e91"
author devteam
date Mon, 02 Mar 2020 06:46:51 -0500
parents e12f68d2cc4e
children 5cbde03c1103
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
7d37cfda8e00 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 34a6c9f94a5722bb7d2f887618aafa410a770e91"
devteam
parents: 4
diff changeset
1 <tool id="fasta_compute_length" name="Compute sequence length" version="1.0.3" profile="16.04">
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
2 <description></description>
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
3 <requirements>
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
4 <requirement type="package" version="3.7">python</requirement>
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
5 </requirements>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
6 <command>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
7 #if $ref.ref_source == 'dbkey':
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
8 cp '${ref.index.fields.len_path}' '$output'
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
9 #else:
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
10 python '$__tool_directory__/fasta_compute_length.py'
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
11 #if $ref.ref_source == 'history':
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
12 '$input'
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
13 #else:
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
14 '${ref.index.fields.path}'
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
15 #end if
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
16 '$output'
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
17 $ref.keep_first
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
18 $ref.keep_first_word
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
19 #end if
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
20 </command>
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
21 <inputs>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
22 <conditional name="ref">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
23 <param name="ref_source" type="select" label="Sequences">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
24 <option value="history" selected="True">From History</option>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
25 <option value="dbkey">Locally Cached (pre-built length files)</option>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
26 <option value="fasta">Locally Cached (full genomes)</option>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
27 </param>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
28 <when value="history">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
29 <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
30 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
31 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
32 label="Strip fasta description from header?"
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
33 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."/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
34 </when>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
35 <when value="dbkey">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
36 <param name="index" type="select" label="Source Genome Build">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
37 <options from_data_table="__dbkeys__"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
38 </param>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
39 </when>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
40 <when value="fasta">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
41 <param name="index" type="select" label="Source Genome Build">
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
42 <options from_data_table="all_fasta"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
43 </param>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
44 <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
45 <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
46 label="Strip fasta description from header?"
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
47 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."/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
48 </when>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
49 </conditional>
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
50
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 </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
52 <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
53 <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
54 </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
55 <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
56 <test>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
57 <param name="ref|input" value="454.fasta" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
58 <param name="ref|keep_first" value="0"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
59 <param name="ref|keep_first_word" value="id_and_desc" />
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
60 <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
61 </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
62
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 <test>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
64 <param name="ref|input" value="extract_genomic_dna_out1.fasta" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
65 <param name="ref|keep_first" value="0"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
66 <param name="ref|keep_first_word" value="id_and_desc" />
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
67 <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
68 </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
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 <test>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
71 <param name="ref|input" value="454.fasta" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
72 <param name="ref|keep_first" value="14"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
73 <param name="ref|keep_first_word" value="id_and_desc" />
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 <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
75 </test>
3
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
76
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
77 <test>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
78 <param name="ref|ref_source" value="fasta" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
79 <param name="ref|index" value="test_id"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
80 <param name="ref|keep_first_word" value="id_only" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
81 <output name="output" file="merged.tab" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
82 </test>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
83
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
84 <test>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
85 <param name="ref|ref_source" value="dbkey" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
86 <param name="ref|index" value="test_id"/>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
87 <output name="output" file="merged.tab" />
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents: 2
diff changeset
88 </test>
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
89 </tests>
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
90 <help><![CDATA[
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
91
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
92 **What it does**
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
93
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
94 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
95
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
96 -----
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
97
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
98 **Example**
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
99
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
100 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
101
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
102 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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
103 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
104 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
105 &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
106 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
107
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
108 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
109
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
110 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
111 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
112
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
113 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
114
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
115 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
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
116 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
117 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
118 >EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
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
119 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
120
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
121 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
122
de2db1bdfbf8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
123 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
124 EYKX4VC 60
0
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
125
ece409f6573c Imported from capsule None
devteam
parents:
diff changeset
126
4
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
devteam
parents: 3
diff changeset
127 ]]></help>
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
128 <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
129 <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
130 </citations>
1
d8cc2c8eef14 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 0
diff changeset
131 </tool>