annotate fastx_collapser.xml @ 2:421f0af4ee95 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:39:04 -0500
parents 13c2d9e8c6d5
children 7ce1891db6f5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
2 <description>sequences</description>
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
3 <requirements>
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
5 </requirements>
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
6 <command>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
7 <![CDATA[
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
8 zcat -f < '$input' | fastx_collapser -v -o '$output'
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
9 #if $input.ext == "fastqsanger":
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
10 -Q 33
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
11 #end if
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
12 ]]>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
13 </command>
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
14
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
15 <inputs>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
16 <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
17 </inputs>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
18 <outputs>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
19 <data format="fasta" name="output" metadata_source="input" />
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
20 </outputs>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
21 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
22 <tests>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
23 <test>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
24 <param name="input" value="fasta_collapser1.fasta" />
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
25 <param name="output" file="fasta_collapser1.out" />
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
26 </test>
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
27 </tests>
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
28 -->
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
29 <help>
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
30 **What it does**
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
31
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
32 This tool collapses identical sequences in a FASTA file into a single sequence.
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
33
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
34 --------
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
35
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
36 **Example**
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
37
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
38 Example Input File (Sequence "ATAT" appears multiple times)::
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
39
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
40 >CSHL_2_FC0042AGLLOO_1_1_605_414
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
41 TGCG
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
42 >CSHL_2_FC0042AGLLOO_1_1_537_759
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
43 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
44 >CSHL_2_FC0042AGLLOO_1_1_774_520
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
45 TGGC
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
46 >CSHL_2_FC0042AGLLOO_1_1_742_502
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
47 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
48 >CSHL_2_FC0042AGLLOO_1_1_781_514
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
49 TGAG
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
50 >CSHL_2_FC0042AGLLOO_1_1_757_487
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
51 TTCA
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
52 >CSHL_2_FC0042AGLLOO_1_1_903_769
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
53 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
54 >CSHL_2_FC0042AGLLOO_1_1_724_499
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
55 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
56
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
57 Example Output file::
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
58
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
59 >1-1
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
60 TGCG
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
61 >2-4
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
62 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
63 >3-1
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
64 TGGC
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
65 >4-1
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
66 TGAG
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
67 >5-1
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
68 TTCA
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
69
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
70 .. class:: infomark
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
71
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
72 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
73
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
74 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
75
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
76 The following output::
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
77
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
78 >2-4
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
79 ATAT
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
80
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
81 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
82
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
83
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
84 ------
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
85
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
87
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
2
421f0af4ee95 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 1
diff changeset
89 </help>
0
e942fd3a76a5 Uploaded tool tarball.
devteam
parents:
diff changeset
90 </tool>