Mercurial > repos > iuc > vardict_java

annotate macros.xml @ 1:e31b6f4d89ad 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/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
author iuc
date Fri, 11 Sep 2020 21:06:52 +0000
parents 7966f5292530
children 6733325083d3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
1 <macros>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
2 <token name="@VERSION_SUFFIX@">0</token>
1
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">1.8.1</token>
0
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
4 <xml name="ref_select">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
5 <conditional name="reference_source">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
6 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
7 <option value="cached" selected="True">Use a built-in genome</option>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
8 <option value="history">Use a genome from the history</option>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
9 </param>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
10 <when value="cached">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
11 <param name="ref_file" type="select" label="Reference Genome File">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
12 <options from_data_table="fasta_indexes"/>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
13 </param>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
14 </when>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
15 <when value="history">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
16 <param name="ref_file" format="fasta" type="data" label="Reference Genome File" />
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
17 </when>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
18 </conditional>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
19 </xml>
1
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
20 <xml name="stdio">
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
21 <stdio>
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
22 <regex match="java.lang.OutOfMemoryError" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
23 </stdio>
e31b6f4d89ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents: 0
diff changeset
24 </xml>
0
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
25 <xml name="input_default">
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
26 <param name="tumor" type="data" format="bam" label="Tumor file" />
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
27 <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
28 </xml>
7966f5292530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff changeset
29 </macros>