Mercurial > repos > dfornika > cgview

annotate reformat_blastn_output.xml @ 8:fece9758fea4 draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
author dfornika
date Fri, 01 Nov 2019 21:20:45 -0400
parents ecd17b1142e6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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1 <tool id="reformat_blastn_output" name="reformat blastn output" version="1.0+galaxy0">
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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2 <description>Reformat blastn output for cgview_xml_builder</description>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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3 <requirements>
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4 </requirements>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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5 <command detect_errors="exit_code">
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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6 <![CDATA[
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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7 awk -F'\t' 'BEGIN {OFS = FS} $2 = $2 FS "match"' '${input}' |
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ecd17b1142e6 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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8 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' |
ecd17b1142e6 planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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9 sed '1i#PROGRAM=blastn'
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5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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10 > '${output}'
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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11 ]]>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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12 </command>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Input" help=""/>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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15 </inputs>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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16 <outputs>
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17 <data name="output" format="tabular"/>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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18 </outputs>
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19 <tests>
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20 </tests>
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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21 <help>
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22 </help>
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23 <citations>
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24 <citation type="bibtex">
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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25 @article{
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26 stothard2004circular,
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27 title={Circular genome visualization and exploration using CGView},
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28 author={Stothard, Paul and Wishart, David S},
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29 journal={Bioinformatics},
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30 volume={21},
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31 number={4},
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32 pages={537--539},
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33 year={2004},
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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34 publisher={Oxford University Press}
5542de6121ac planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/cgview commit 423cf96266f6ac433052ff72edb1397502313010-dirty
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35 }
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36 </citation>
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37 </citations>
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38 </tool>