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annotate macros.xml @ 3:08de71d3ea76 draft default tip

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planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7-dirty
author mvdbeek
date Fri, 27 Jan 2017 08:16:01 -0500
parents ff6683f8e9a1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
1 <macros>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
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2 <xml name="requirements">
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
3 <requirements>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
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4 <requirement type="package" version="0.8.0">tepid</requirement>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
5 <yield/>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
6 </requirements>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
7 </xml>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
8 <token name="@WRAPPER_VERSION@">0.8.0</token>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
9 <token name="@REFERENCES@">
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
10 <![CDATA[
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
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11 ------
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
12 This tool is part of the `TEPID`_ pipeline from the `Lister laboratory`_.
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
13 .. _TEPID package: https://github.com/ListerLab/TEPID
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
14 .. _Lister laboratory http://listerlab.org/
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
15 ]]>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
16 </token>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
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17 <token name="@PROC@">-p \$GALAXY_SLOTS</token>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
18 <token name="@NAME@">-n '$bowtie2_bam.element_identifier'</token>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
19 <token name="@LINK_CONC@"><![CDATA[
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
20 ln -f -s '$bowtie2_bam' conc.bam &&
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
21 ln -f -s '$bowtie2_bam.metadata.bam_index' conc.bam.bai &&
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
22 ]]></token>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
23 <xml name="citations">
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
24 <citations>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
25 <citation type="doi">10.7554/eLife.20777</citation>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
26 <yield />
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
27 </citations>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
28 </xml>
ff6683f8e9a1 planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
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29 </macros>