Mercurial > repos > iuc > snpeff

annotate snpEff_macros.xml @ 4:698ef30638a8 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/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
author iuc
date Fri, 16 Sep 2016 13:06:42 -0400
parents b24873564cf6
children 7adfd0589f49
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
1 <macros>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
2 <xml name="requirements">
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
3 <requirements>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
4 <requirement type="package" version="4.1">snpEff</requirement>
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
5 </requirements>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
6 </xml>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
7 <xml name="stdio">
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
8 <stdio>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Error" />
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
11 </stdio>
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
12 </xml>
4
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
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>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
14 <xml name="version_command">
4
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
15 <version_command><![CDATA[
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
16 if [ -z "$SNPEFF_JAR_PATH" ]; then
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
698ef30638a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
iuc
parents: 3
diff changeset
19 ]]></version_command>
3
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
20 </xml>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
21 <token name="@WRAPPER_VERSION@">4.1</token>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
22 <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 1
diff changeset
23 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
24 <token name="@EXTERNAL_DOCUMENTATION@">
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
25
1
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
26 For details about this tool, please go to:
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
27 http://snpeff.sourceforge.net/SnpEff_manual.html
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
28
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
29 </token>
1
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
30 <xml name="citations">
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
31 <citations>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
32 <citation type="doi">10.4161/fly.19695</citation>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
33 <yield />
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
34 </citations>
500832f27cbc Uploaded
iuc
parents: 0
diff changeset
35 </xml>
0
e8adfc4c0a6b Uploaded
iuc
parents:
diff changeset
36 </macros>