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comparison gbToFasta.xml @ 1:da5fba0ed4fc draft

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planemo upload
author yating-l
date Fri, 03 Feb 2017 11:30:42 -0500
parents e51fb8c5bb1c
children cabe1df9d31a
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0:e51fb8c5bb1c 1:da5fba0ed4fc
3 <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description> 3 <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> 5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 gbToFaRa 8 gbToFaRa
9 /dev/null 9 /dev/null
10 '${output_fa}' 10 '${outputfa}'
11 output_ra 11 outputra
12 output_ta 12 outputta
13 '${gbfile}' 13 '${gbfile}'
14 #if $cds == "yes" 14 #if $cds == "yes"
15 && raToTab 15 && raToTab
16 -cols=acc,cds 16 -cols=acc,cds
17 output_ra 17 outputra
18 '${output_cds}' 18 '${outputcds}'
19 #end if 19 #end if
20
21 ]]></command> 20 ]]></command>
22 <inputs> 21 <inputs>
23 <param type="data" name="gbfile" format="genbank" /> 22 <param type="data" name="gbfile" format="genbank" />
24 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" > 23 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" >
25 <option value="yes">Yes</option> 24 <option value="yes">Yes</option>
26 <option value="no">No</option> 25 <option value="no">No</option>
27 </param> 26 </param>
28 27
29 </inputs> 28 </inputs>
30 <outputs> 29 <outputs>
31 <data format="fasta" name="output_fa" label="${gbfile.name}:fasta"></data> 30 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
32 <data format="fasta" name="output_cds" label="${gbfile.name}:cds"> 31 <data format="fasta" name="outputcds" label="${tool.name} on ${on_string}:cds">
33 <filter>cds == "yes"</filter> 32 <filter>cds == "yes"</filter>
34 </data> 33 </data>
35 </outputs> 34 </outputs>
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> 37 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
39 <param name="cds" value="yes" /> 38 <param name="cds" value="yes" />
40 <output name="output_fa" value="Gallus_gallus_RefSeq.fa" /> 39 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
41 <output name="output_cds" value="Gallus_gallus_RefSeq.cds" /> 40 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
42 </test> 41 </test>
43 <test> 42 <test>
44 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> 43 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
45 <param name="cds" value="no" /> 44 <param name="cds" value="no" />
46 <output name="output_fa" value="Gallus_gallus_RefSeq.fa" /> 45 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
47 </test> 46 </test>
48 </tests> 47 </tests>
49 <help> 48 <help>
50 <![CDATA[ 49 <![CDATA[
51 gbToFasta 50 gbToFasta
60 usage: 59 usage:
61 gbToFaRa filterFile faFile raFile taFile genBankFile(s) 60 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
62 where filterFile is definition of which records and fields 61 where filterFile is definition of which records and fields
63 use /dev/null if you want no filtering. 62 use /dev/null if you want no filtering.
64 63
65 gbToFaRa /dev/null ${gbfile.fa} \ 64 gbToFaRa /dev/null gbfile.fa \
66 ${gbfile.ra} ${gbfile.ta} ${gbfile} 65 gbfile.ra gbfile.ta gbfile
67 66
68 Create table with coding regions information for each mRNA record 67 Create table with coding regions information for each mRNA record
69 ----------------------------------------------------------------- 68 -----------------------------------------------------------------
70 raToTab - Convert ra file to table. 69 raToTab - Convert ra file to table.
71 raToTab -cols=acc,cds ${gbfile.ra} ${gbfile.cds} 70 raToTab -cols=acc,cds gbfile.ra gbfile.cds
72 71
73 Source code: 72 Source code:
74 ============ 73 ============
75 74
76 http://hgdownload.cse.ucsc.edu/admin/exe/ 75 http://hgdownload.cse.ucsc.edu/admin/exe/
77 76
78 ]]></help> 77 ]]></help>
79 <citations> 78 <citations>
80 <citation type="bibtex">@article{kent2002blat, 79 <citation type="bibtex">@article{kent2002blat,
81 title={BLAT—the BLAST-like alignment tool}, 80 title={BLAT—the BLAST-like alignment tool},
82 author={Kent, W James}, 81 author={Kent, W James},
83 journal={Genome research}, 82 journal={Genome research},
84 volume={12}, 83 volume={12},
85 number={4}, 84 number={4},
86 pages={656--664}, 85 pages={656--664},
87 year={2002}, 86 year={2002},
88 publisher={Cold Spring Harbor Lab} 87 publisher={Cold Spring Harbor Lab}
89 }</citation> 88 }</citation>
90 </citations> 89 </citations>
90
91 </tool> 91 </tool>
92 92
93 93
94 94
95 95