Mercurial > repos > yating-l > gbtofasta
annotate gbToFasta.xml @ 3:894d96efad6d draft
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| author | yating-l |
|---|---|
| date | Mon, 05 Jun 2017 12:00:08 -0400 |
| parents | cabe1df9d31a |
| children | 3568235c44bf |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="gbtofasta" name="gbToFasta" version="1.0"> | |
| 3 <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 1 | 8 gbToFaRa |
| 0 | 9 /dev/null |
| 1 | 10 '${outputfa}' |
| 11 outputra | |
| 12 outputta | |
| 0 | 13 '${gbfile}' |
| 14 #if $cds == "yes" | |
| 15 && raToTab | |
| 16 -cols=acc,cds | |
| 1 | 17 outputra |
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894d96efad6d
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18 cds_file |
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894d96efad6d
planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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19 && python $__tool_directory__/filter.py -f cds_file -o '${outputcds}' |
| 0 | 20 #end if |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param type="data" name="gbfile" format="genbank" /> | |
| 24 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" > | |
| 25 <option value="yes">Yes</option> | |
| 26 <option value="no">No</option> | |
| 27 </param> | |
| 28 | |
| 29 </inputs> | |
| 30 <outputs> | |
| 1 | 31 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data> |
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2
cabe1df9d31a
planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
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32 <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds"> |
| 0 | 33 <filter>cds == "yes"</filter> |
| 34 </data> | |
| 35 </outputs> | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 39 <param name="cds" value="yes" /> | |
| 1 | 40 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
| 41 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" /> | |
| 0 | 42 </test> |
| 43 <test> | |
| 44 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 45 <param name="cds" value="no" /> | |
| 1 | 46 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
| 0 | 47 </test> |
| 48 </tests> | |
| 49 <help> | |
| 50 <![CDATA[ | |
| 51 gbToFasta | |
| 52 ========= | |
| 53 | |
| 54 Convert GenBank records to fasta | |
| 55 --------------------------------- | |
| 56 | |
| 57 gbToFaRa - Convert GenBank flat format file to an fa file containing | |
| 58 the sequence data, an ra file containing other relevant info and | |
| 59 a ta file containing summary statistics. | |
| 60 usage: | |
| 61 gbToFaRa filterFile faFile raFile taFile genBankFile(s) | |
| 62 where filterFile is definition of which records and fields | |
| 63 use /dev/null if you want no filtering. | |
| 64 | |
| 1 | 65 gbToFaRa /dev/null gbfile.fa \ |
| 66 gbfile.ra gbfile.ta gbfile | |
| 0 | 67 |
| 68 Create table with coding regions information for each mRNA record | |
| 69 ----------------------------------------------------------------- | |
| 70 raToTab - Convert ra file to table. | |
| 1 | 71 raToTab -cols=acc,cds gbfile.ra gbfile.cds |
| 0 | 72 |
| 73 Source code: | |
| 74 ============ | |
| 75 | |
| 76 http://hgdownload.cse.ucsc.edu/admin/exe/ | |
| 77 | |
| 1 | 78 ]]></help> |
| 79 <citations> | |
| 80 <citation type="bibtex">@article{kent2002blat, | |
| 81 title={BLAT—the BLAST-like alignment tool}, | |
| 82 author={Kent, W James}, | |
| 83 journal={Genome research}, | |
| 84 volume={12}, | |
| 85 number={4}, | |
| 86 pages={656--664}, | |
| 87 year={2002}, | |
| 88 publisher={Cold Spring Harbor Lab} | |
| 89 }</citation> | |
| 90 </citations> | |
| 91 | |
| 0 | 92 </tool> |
| 93 | |
| 94 | |
| 95 | |
| 96 | |
| 97 |