Mercurial > repos > yating-l > gbtofasta
annotate gbToFasta.xml @ 4:3568235c44bf draft
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| author | yating-l |
|---|---|
| date | Tue, 08 Aug 2017 17:53:39 -0400 |
| parents | 894d96efad6d |
| children | e195691d3e71 |
| 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}' |
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14 && |
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15 raToTab |
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16 -cols=acc,def |
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17 outputra |
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18 outputinfo |
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19 && |
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20 ixIxx |
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21 outputinfo |
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22 ${index_ix} |
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23 index_ixx |
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24 |
| 0 | 25 #if $cds == "yes" |
| 26 && raToTab | |
| 27 -cols=acc,cds | |
| 1 | 28 outputra |
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29 cds_file |
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30 && python $__tool_directory__/filter.py -f cds_file -o '${outputcds}' |
| 0 | 31 #end if |
| 32 ]]></command> | |
| 33 <inputs> | |
| 34 <param type="data" name="gbfile" format="genbank" /> | |
| 35 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" > | |
| 36 <option value="yes">Yes</option> | |
| 37 <option value="no">No</option> | |
| 38 </param> | |
| 39 | |
| 40 </inputs> | |
| 41 <outputs> | |
| 1 | 42 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data> |
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43 <data format="txt" name="index_ix" label="${tool.name} on ${on_string}:txt"></data> |
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44 <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds"> |
| 0 | 45 <filter>cds == "yes"</filter> |
| 46 </data> | |
| 47 </outputs> | |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 51 <param name="cds" value="yes" /> | |
| 1 | 52 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
| 53 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" /> | |
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54 <output name="index_ix" value="Gallus_gallus_RefSeq.ix" /> |
| 0 | 55 </test> |
| 56 <test> | |
| 57 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 58 <param name="cds" value="no" /> | |
| 1 | 59 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
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3568235c44bf
planemo upload commit 4737b5365c135058ff6dc65a3d9f249b11f1751a-dirty
yating-l
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60 <output name="index_ix" value="Gallus_gallus_RefSeq.ix" /> |
| 0 | 61 </test> |
| 62 </tests> | |
| 63 <help> | |
| 64 <![CDATA[ | |
| 65 gbToFasta | |
| 66 ========= | |
| 67 | |
| 68 Convert GenBank records to fasta | |
| 69 --------------------------------- | |
| 70 | |
| 71 gbToFaRa - Convert GenBank flat format file to an fa file containing | |
| 72 the sequence data, an ra file containing other relevant info and | |
| 73 a ta file containing summary statistics. | |
| 74 usage: | |
| 75 gbToFaRa filterFile faFile raFile taFile genBankFile(s) | |
| 76 where filterFile is definition of which records and fields | |
| 77 use /dev/null if you want no filtering. | |
| 78 | |
| 1 | 79 gbToFaRa /dev/null gbfile.fa \ |
| 80 gbfile.ra gbfile.ta gbfile | |
| 0 | 81 |
| 82 Create table with coding regions information for each mRNA record | |
| 83 ----------------------------------------------------------------- | |
| 84 raToTab - Convert ra file to table. | |
| 1 | 85 raToTab -cols=acc,cds gbfile.ra gbfile.cds |
| 0 | 86 |
| 87 Source code: | |
| 88 ============ | |
| 89 | |
| 90 http://hgdownload.cse.ucsc.edu/admin/exe/ | |
| 91 | |
| 1 | 92 ]]></help> |
| 93 <citations> | |
| 94 <citation type="bibtex">@article{kent2002blat, | |
| 95 title={BLAT—the BLAST-like alignment tool}, | |
| 96 author={Kent, W James}, | |
| 97 journal={Genome research}, | |
| 98 volume={12}, | |
| 99 number={4}, | |
| 100 pages={656--664}, | |
| 101 year={2002}, | |
| 102 publisher={Cold Spring Harbor Lab} | |
| 103 }</citation> | |
| 104 </citations> | |
| 105 | |
| 0 | 106 </tool> |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 |