Mercurial > repos > yating-l > gbtofasta

annotate gbToFasta.xml @ 7:57e30c6c0aa4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 418d3a27a673cef3f350e514fb6101fcde009b9d
author yating-l
date Mon, 06 Nov 2017 15:45:26 -0500
parents 97499dcb77fa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
1 <?xml version="1.0"?>
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
2 <tool id="gbtofasta" name="gbToFasta" version="2.0">
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
3 <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
4 <requirements>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
6 </requirements>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
8 gbToFaRa
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
9 /dev/null
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
10 '${outputfa}'
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
11 outputra
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
12 outputta
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
13 '${gbfile}'
4
3568235c44bf planemo upload commit 4737b5365c135058ff6dc65a3d9f249b11f1751a-dirty
yating-l
parents: 3
diff changeset
14
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
15 #if $cds == "yes"
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
16 && raToTab
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
17 -cols=acc,cds
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
18 outputra
3
894d96efad6d planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
parents: 2
diff changeset
19 cds_file
894d96efad6d planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
parents: 2
diff changeset
20 && python $__tool_directory__/filter.py -f cds_file -o '${outputcds}'
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
21 #end if
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
22
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
23 #if $trix == "yes"
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
24 && raToTab
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
25 -cols=acc,def
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
26 outputra
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
27 outputinfo
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
28 && ixIxx
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
29 outputinfo
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
30 ${index_ix}
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
31 ${index_ixx}
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
32 #end if
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
33
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
34 ]]></command>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
35 <inputs>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
36 <param type="data" name="gbfile" format="genbank" />
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
37 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" >
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
38 <option value="yes">Yes</option>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
39 <option value="no">No</option>
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
40 </param>
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
41 <param type="select" name="trix" label="Create a Trix index" >
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
42 <option value="yes">Yes</option>
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
43 <option value="no">No</option>
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
44 </param>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
45 </inputs>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
46 <outputs>
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
47 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
2
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents: 1
diff changeset
48 <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds">
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
49 <filter>cds == "yes"</filter>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
50 </data>
6
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
51 <collection name="trix_index" type="list" label="${tool.name} on ${on_string}:Trix index">
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
52 <filter>trix == "yes"</filter>
7
57e30c6c0aa4 planemo upload commit 418d3a27a673cef3f350e514fb6101fcde009b9d
yating-l
parents: 6
diff changeset
53 <data name="index_ix" format="txt" />
57e30c6c0aa4 planemo upload commit 418d3a27a673cef3f350e514fb6101fcde009b9d
yating-l
parents: 6
diff changeset
54 <data name="index_ixx" format="txt" />
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
55 </collection>
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
56 </outputs>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
57 <tests>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
58 <test>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
59 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
60 <param name="cds" value="yes" />
6
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
61 <param name="trix" value="yes" />
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
62 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
63 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
6
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
64 <output_collection name="trix_index" type="list">
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
65 <element name="index_ix" value="Gallus_gallus_RefSeq.ix" />
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
66 <element name="index_ixx" value="Gallus_gallus_RefSeq.ixx" />
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
67 </output_collection>
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
68 </test>
6
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
69
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
70 <test>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
71 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
72 <param name="cds" value="no" />
6
97499dcb77fa planemo upload commit d860eb554edd28f07d8586e7fb2599514937873a
yating-l
parents: 5
diff changeset
73 <param name="trix" value="no" />
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
74 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
75 </test>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
76 </tests>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
77 <help>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
78 <![CDATA[
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
79 gbToFasta
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
80 =========
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
81
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
82 Convert GenBank records to fasta
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
83 ---------------------------------
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
84
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
85 gbToFaRa - Convert GenBank flat format file to an fa file containing
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
86 the sequence data, an ra file containing other relevant info and
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
87 a ta file containing summary statistics.
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
88 usage:
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
89 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
90 where filterFile is definition of which records and fields
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
91 use /dev/null if you want no filtering.
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
92
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
93 gbToFaRa /dev/null gbfile.fa \
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
94 gbfile.ra gbfile.ta gbfile
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
95
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
96 Create table with coding regions information for each mRNA record
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
97 -----------------------------------------------------------------
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
98 raToTab - Convert ra file to table.
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
99 raToTab -cols=acc,cds gbfile.ra gbfile.cds
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
100
5
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
101 Create a Trix index with coding regions information
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
102 ---------------------------------------------------
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
103 ixIxx - Create indices for simple line-oriented file of format
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
104
e195691d3e71 planemo upload commit 10faac43ed16e0bd479f2e9a7d76ccd08b2a5af8-dirty
yating-l
parents: 4
diff changeset
105
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
106 Source code:
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
107 ============
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
108
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
109 http://hgdownload.cse.ucsc.edu/admin/exe/
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
110
1
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
111 ]]></help>
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
112 <citations>
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
113 <citation type="bibtex">@article{kent2002blat,
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
114 title={BLAT—the BLAST-like alignment tool},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
115 author={Kent, W James},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
116 journal={Genome research},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
117 volume={12},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
118 number={4},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
119 pages={656--664},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
120 year={2002},
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
121 publisher={Cold Spring Harbor Lab}
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
122 }</citation>
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
123 </citations>
da5fba0ed4fc planemo upload
yating-l
parents: 0
diff changeset
124
0
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
125 </tool>
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
126
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
127
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
128
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
129
e51fb8c5bb1c planemo upload
yating-l
parents:
diff changeset
130