Mercurial > repos > dfornika > cgview_reformat_blastn_output

annotate reformat_blastn_output.xml @ 0:90ac002b2098 draft default tip

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