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annotate gbToFasta.xml @ 5:e195691d3e71 draft
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| author | yating-l |
|---|---|
| date | Thu, 28 Sep 2017 16:25:57 -0400 |
| parents | 3568235c44bf |
| children | 97499dcb77fa |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
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2 <tool id="gbtofasta" name="gbToFasta" version="2.0"> |
| 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 |
| 0 | 15 #if $cds == "yes" |
| 16 && raToTab | |
| 17 -cols=acc,cds | |
| 1 | 18 outputra |
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19 cds_file |
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20 && python $__tool_directory__/filter.py -f cds_file -o '${outputcds}' |
| 0 | 21 #end if |
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22 |
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23 #if $trix == "yes" |
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24 && raToTab |
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25 -cols=acc,def |
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26 outputra |
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27 outputinfo |
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28 && ixIxx |
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29 outputinfo |
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30 ${index_ix} |
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31 ${index_ixx} |
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32 #end if |
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33 |
| 0 | 34 ]]></command> |
| 35 <inputs> | |
| 36 <param type="data" name="gbfile" format="genbank" /> | |
| 37 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" > | |
| 38 <option value="yes">Yes</option> | |
| 39 <option value="no">No</option> | |
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40 </param> |
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41 <param type="select" name="trix" label="Create a Trix index" > |
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42 <option value="yes">Yes</option> |
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43 <option value="no">No</option> |
| 0 | 44 </param> |
| 45 </inputs> | |
| 46 <outputs> | |
| 1 | 47 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data> |
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48 <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds"> |
| 0 | 49 <filter>cds == "yes"</filter> |
| 50 </data> | |
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51 <collection name="trix_index" type="list" label="Trix index"> |
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52 <filter>trix == "yes"</filter> |
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53 <data name="index_ix" format="txt" from_work_dir="output.ix"/> |
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54 <data name="index_ixx" format="txt" from_work_dir="output.ixx" /> |
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55 </collection> |
| 0 | 56 </outputs> |
| 57 <tests> | |
| 58 <test> | |
| 59 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 60 <param name="cds" value="yes" /> | |
| 1 | 61 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
| 62 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" /> | |
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63 <output name="index_ix" value="Gallus_gallus_RefSeq.ix" /> |
| 0 | 64 </test> |
| 65 <test> | |
| 66 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" /> | |
| 67 <param name="cds" value="no" /> | |
| 1 | 68 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" /> |
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69 <output name="index_ix" value="Gallus_gallus_RefSeq.ix" /> |
| 0 | 70 </test> |
| 71 </tests> | |
| 72 <help> | |
| 73 <![CDATA[ | |
| 74 gbToFasta | |
| 75 ========= | |
| 76 | |
| 77 Convert GenBank records to fasta | |
| 78 --------------------------------- | |
| 79 | |
| 80 gbToFaRa - Convert GenBank flat format file to an fa file containing | |
| 81 the sequence data, an ra file containing other relevant info and | |
| 82 a ta file containing summary statistics. | |
| 83 usage: | |
| 84 gbToFaRa filterFile faFile raFile taFile genBankFile(s) | |
| 85 where filterFile is definition of which records and fields | |
| 86 use /dev/null if you want no filtering. | |
| 87 | |
| 1 | 88 gbToFaRa /dev/null gbfile.fa \ |
| 89 gbfile.ra gbfile.ta gbfile | |
| 0 | 90 |
| 91 Create table with coding regions information for each mRNA record | |
| 92 ----------------------------------------------------------------- | |
| 93 raToTab - Convert ra file to table. | |
| 1 | 94 raToTab -cols=acc,cds gbfile.ra gbfile.cds |
| 0 | 95 |
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96 Create a Trix index with coding regions information |
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97 --------------------------------------------------- |
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98 ixIxx - Create indices for simple line-oriented file of format |
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99 |
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100 |
| 0 | 101 Source code: |
| 102 ============ | |
| 103 | |
| 104 http://hgdownload.cse.ucsc.edu/admin/exe/ | |
| 105 | |
| 1 | 106 ]]></help> |
| 107 <citations> | |
| 108 <citation type="bibtex">@article{kent2002blat, | |
| 109 title={BLAT—the BLAST-like alignment tool}, | |
| 110 author={Kent, W James}, | |
| 111 journal={Genome research}, | |
| 112 volume={12}, | |
| 113 number={4}, | |
| 114 pages={656--664}, | |
| 115 year={2002}, | |
| 116 publisher={Cold Spring Harbor Lab} | |
| 117 }</citation> | |
| 118 </citations> | |
| 119 | |
| 0 | 120 </tool> |
| 121 | |
| 122 | |
| 123 | |
| 124 | |
| 125 |