Mercurial > repos > gga > tripal_expression_add_biomaterial

annotate expression_add_biomaterial.xml @ 0:0f6c9307d6f3 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author gga
date Mon, 25 Feb 2019 05:56:41 -0500
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0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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1 <?xml version="1.0"?>
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2 <tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.0">
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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3 <description>in Tripal</description>
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4 <macros>
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5 <import>macros.xml</import>
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="tripal.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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10 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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11
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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12 &&
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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14 cp '${file_path}' "\${tmp_dir}/biomaterial_input"
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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16 &&
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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18 @AUTH@
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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19
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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20 tripaille expression add_biomaterial
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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21 '$organism_id'
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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22 "\${tmp_dir}/biomaterial_input"
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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23 '$file_path.extension'
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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24
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25 &&
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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27 echo "Data loaded" > $results
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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28 ]]></command>
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29 <inputs>
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30 <!-- arguments -->
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31 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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32 <param name="file_path" label="Biomaterial description sheet" argument="file_path" type="data" format="xml,tsv,csv" help="A file describing the biomaterial" />
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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33 </inputs>
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34 <outputs>
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35 <data format="txt" name="results"/>
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36 </outputs>
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37 <help>
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38 Add a new biomaterial to the database
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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39
0f6c9307d6f3 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
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40 @HELP@
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41 </help>
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42 </tool>