Mercurial > repos > mvdbeek > tepid_discover

annotate macros.xml @ 0:a5ef6470e54d draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
author mvdbeek
date Thu, 15 Dec 2016 08:33:53 -0500
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a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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1 <macros>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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2 <xml name="requirements">
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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3 <requirements>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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4 <requirement type="package" version="0.8.0">tepid</requirement>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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5 <yield/>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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6 </requirements>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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7 </xml>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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8 <token name="@WRAPPER_VERSION@">0.8.0</token>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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9 <token name="@REFERENCES@">
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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10 <![CDATA[
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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11 ------
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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12 This tool is part of the `TEPID`_ pipeline from the `Lister laboratory`_.
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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13 .. _TEPID package: https://github.com/ListerLab/TEPID
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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14 .. _Lister laboratory http://listerlab.org/
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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15 ]]>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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16 </token>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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17 <token name="@PROC@">-p \$GALAXY_SLOTS</token>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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18 <token name="@NAME@">-n '$bowtie2_bam.element_identifier'</token>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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19 <token name="@LINK_CONC@"><![CDATA[
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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20 ln -f -s '$bowtie2_bam' conc.bam &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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21 ln -f -s '$bowtie2_bam.metadata.bam_index' conc.bam.bai &&
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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22 ]]></token>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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23 <xml name="citations">
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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24 <citations>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
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25 <citation type="doi">10.7554/eLife.20777</citation>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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26 <yield />
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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27 </citations>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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28 </xml>
a5ef6470e54d planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
mvdbeek
parents:
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29 </macros>