Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_macros.xml @ 278:02f54bf45aaf 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_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:05:47 -0500
parents 6c1a0c6cf28c
children 2c41c1631d1c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
1 <macros>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
2 <xml name="requirements">
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
3 <requirements>
278
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
diff changeset
4 <requirement type="package" version="4.1">snpsift</requirement>
0
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
5 </requirements>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
6 </xml>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
7 <xml name="stdio">
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
8 <stdio>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Error" />
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
11 </stdio>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
12 </xml>
278
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
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>
277
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 0
diff changeset
14 <xml name="version_command">
278
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
diff changeset
15 <version_command><![CDATA[
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
diff changeset
16 if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
diff changeset
17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
02f54bf45aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 277
diff changeset
18 ]]></version_command>
277
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 0
diff changeset
19 </xml>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents: 0
diff changeset
20 <token name="@WRAPPER_VERSION@">4.1</token>
0
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
21 <token name="@EXTERNAL_DOCUMENTATION@">
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
22
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
23 For details about this tool, please go to:
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
24 http://snpeff.sourceforge.net/SnpEff_manual.html
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
25
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
26 </token>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
27 <xml name="citations">
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
28 <citations>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
29 <citation type="doi">10.3389/fgene.2012.00035</citation>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
30 <yield />
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
31 </citations>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
32 </xml>
7fe1fad13841 Uploaded
iuc
parents:
diff changeset
33 </macros>