Mercurial > repos > iuc > snpsift_genesets

annotate snpSift_macros.xml @ 2:9ba6e2c298ab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
author iuc
date Mon, 19 Sep 2016 14:43:55 -0400
parents 0af41de4eda1
children 847db7b39bdc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
1 <macros>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
2 <xml name="requirements">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
3 <requirements>
1
0af41de4eda1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
4 <requirement type="package" version="4.1">snpEff</requirement>
0
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
5 </requirements>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
6 </xml>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
7 <xml name="stdio">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
8 <stdio>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Error" />
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
11 </stdio>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
12 </xml>
2
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
13 <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
1
0af41de4eda1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
14 <xml name="version_command">
2
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
15 <version_command><![CDATA[
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
16 if [ -z "$SNPEFF_JAR_PATH" ]; then
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
9ba6e2c298ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
iuc
parents: 1
diff changeset
19 ]]></version_command>
1
0af41de4eda1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
20 </xml>
0af41de4eda1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
21 <token name="@WRAPPER_VERSION@">4.1</token>
0
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
22 <token name="@EXTERNAL_DOCUMENTATION@">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
23
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
24 For details about this tool, please go to:
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
25 http://snpeff.sourceforge.net/SnpEff_manual.html
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
26
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
27 </token>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
28 <token name="@CITATION_SECTION@">------
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
29
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
30 **Citation**
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
31
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
32 For the underlying tool, please cite the following two publications:
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
33
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
34 SnpSift citation:
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
35 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
36
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
37 </token>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
38 <xml name="citations">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
39 <citations>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
40 <citation type="doi">10.3389/fgene.2012.00035</citation>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
41 <yield />
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
42 </citations>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
43 </xml>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
44 </macros>