Mercurial > repos > refinery-platform > picard_merge_sam_files
comparison picard_MergeSamFiles.xml @ 4:2c6b2c6ee3bb draft
planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 2137a21daebbb1cf755e8bf99fae7f5a77b07f87-dirty
| author | refinery-platform |
|---|---|
| date | Mon, 04 Dec 2017 10:16:33 -0500 |
| parents | 40d9376df6d6 |
| children | 28f273969b5e |
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| 3:a01e30f7777f | 4:2c6b2c6ee3bb |
|---|---|
| 1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> | 1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> |
| 2 <description>merges multiple SAM/BAM datasets into one</description> | 2 <description>merges multiple SAM/BAM datasets into one</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>picard_macros.xml</import> | 4 <import>picard_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 8 @java_options@ | 7 @java_options@ |
| 9 #for $index, $listCollection in enumerate($inputList): | 8 #for $index, $listCollection in enumerate($inputList): |
| 10 && | 9 && |
| 11 picard | 10 java -jar \$JAVA_JAR_PATH/picard.jar |
| 12 MergeSamFiles | 11 MergeSamFiles |
| 13 | 12 |
| 14 #for $element in $listCollection: | 13 #for $element in $listCollection: |
| 15 INPUT="${element}" | 14 INPUT="${element}" |
| 16 #end for | 15 #end for |