Mercurial > repos > iuc > vardict_java
annotate macros.xml @ 3:e0734e88a104 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
author | iuc |
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date | Thu, 27 Jan 2022 15:19:23 +0000 |
parents | d262577e04b0 |
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0
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
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1 <macros> |
3
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
2
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2 <token name="@VERSION_SUFFIX@">1</token> |
2
d262577e04b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e"
iuc
parents:
1
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3 <token name="@TOOL_VERSION@">1.8.3</token> |
0
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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4 <xml name="ref_select"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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5 <conditional name="reference_source"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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6 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file"> |
2
d262577e04b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e"
iuc
parents:
1
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changeset
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7 <option value="cached" selected="true">Use a built-in genome</option> |
0
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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8 <option value="history">Use a genome from the history</option> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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9 </param> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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10 <when value="cached"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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11 <param name="ref_file" type="select" label="Reference Genome File"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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12 <options from_data_table="fasta_indexes"/> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
|
13 </param> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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14 </when> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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15 <when value="history"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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16 <param name="ref_file" format="fasta" type="data" label="Reference Genome File" /> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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17 </when> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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18 </conditional> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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19 </xml> |
1
5f756651a1bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents:
0
diff
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20 <xml name="stdio"> |
5f756651a1bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents:
0
diff
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21 <stdio> |
5f756651a1bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents:
0
diff
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22 <regex match="java.lang.OutOfMemoryError" source="stderr" level="fatal_oom" description="Out of memory error occurred" /> |
5f756651a1bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents:
0
diff
changeset
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23 </stdio> |
5f756651a1bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
iuc
parents:
0
diff
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24 </xml> |
0
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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25 <xml name="input_default"> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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26 <param name="tumor" type="data" format="bam" label="Tumor file" /> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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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)" /> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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28 </xml> |
2975b29bcaa1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
iuc
parents:
diff
changeset
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29 </macros> |