Mercurial > repos > iuc > snpsift_genesets

annotate snpSift_macros.xml @ 3:847db7b39bdc 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_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:09 -0500
parents 9ba6e2c298ab
children d12a810c837e
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>
3
847db7b39bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 2
diff changeset
4 <requirement type="package" version="4.1">snpsift</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>
3
847db7b39bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 2
diff changeset
13 <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); 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[
3
847db7b39bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 2
diff changeset
16 if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
847db7b39bdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 2
diff changeset
17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
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
18 ]]></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
19 </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
20 <token name="@WRAPPER_VERSION@">4.1</token>
0
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
21 <token name="@EXTERNAL_DOCUMENTATION@">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
22
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
23 For details about this tool, please go to:
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
24 http://snpeff.sourceforge.net/SnpEff_manual.html
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
25
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
26 </token>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
27 <xml name="citations">
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
28 <citations>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
29 <citation type="doi">10.3389/fgene.2012.00035</citation>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
30 <yield />
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
31 </citations>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
32 </xml>
9e6fa49c1077 Uploaded
iuc
parents:
diff changeset
33 </macros>