Mercurial > repos > dfornika > cgview_reformat_blastn_output
comparison reformat_blastn_output.xml @ 0:90ac002b2098 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
| author | dfornika |
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| date | Thu, 12 Dec 2019 19:44:51 +0000 |
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| children |
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| -1:000000000000 | 0:90ac002b2098 |
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| 1 <tool id="cgview_reformat_blastn_output" name="reformat blastn output for cgview XML builder" version="1.0+galaxy0"> | |
| 2 <description>Reformat blastn output for cgview_xml_builder</description> | |
| 3 <command detect_errors="exit_code"> | |
| 4 <![CDATA[ | |
| 5 awk -F'\t' 'BEGIN {OFS = FS} $2 = $2 FS "match"' '${input}' | | |
| 6 sed '1iquery_id\tmatch_id\tmatch_description\t%_identity\talignment_length\tmismatches\tgap_openings\tq_start\tq_end\ts_start\ts_end\tevalue\tbit_score' | | |
| 7 sed '1i#PROGRAM=blastn' | |
| 8 > '${output}' | |
| 9 ]]> | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="input" type="data" format="tabular" label="Input" help=""/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="output" format="tabular"/> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 </tests> | |
| 19 <help> | |
| 20 </help> | |
| 21 <citations> | |
| 22 <citation type="bibtex"> | |
| 23 @article{ | |
| 24 stothard2004circular, | |
| 25 title={Circular genome visualization and exploration using CGView}, | |
| 26 author={Stothard, Paul and Wishart, David S}, | |
| 27 journal={Bioinformatics}, | |
| 28 volume={21}, | |
| 29 number={4}, | |
| 30 pages={537--539}, | |
| 31 year={2004}, | |
| 32 publisher={Oxford University Press} | |
| 33 } | |
| 34 </citation> | |
| 35 </citations> | |
| 36 </tool> |