Mercurial > repos > iuc > samtools_view
comparison macros.xml @ 1:6ade12d94f9a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
| author | iuc |
|---|---|
| date | Tue, 25 Sep 2018 04:21:24 -0400 |
| parents | 00d1f08bdcdc |
| children | 02afb5ea2fce |
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| 0:00d1f08bdcdc | 1:6ade12d94f9a |
|---|---|
| 65 ]]></token> | 65 ]]></token> |
| 66 <token name="@ADDTHREADS@"><![CDATA[ | 66 <token name="@ADDTHREADS@"><![CDATA[ |
| 67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) | 67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) |
| 68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && | 68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && |
| 69 ]]></token> | 69 ]]></token> |
| 70 | |
| 71 <token name="@ADDMEMORY@"><![CDATA[ | |
| 72 ##compute the number of memory available to samtools sort (-m) | |
| 73 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 | |
| 74 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && | |
| 75 ((addmemory=addmemory*75/100)) && | |
| 76 ]]></token> | |
| 70 <xml name="flag_options"> | 77 <xml name="flag_options"> |
| 71 <option value="1">read is paired</option> | 78 <option value="1">read is paired</option> |
| 72 <option value="2">read is mapped in a proper pair</option> | 79 <option value="2">read is mapped in a proper pair</option> |
| 73 <option value="4">read is unmapped</option> | 80 <option value="4">read is unmapped</option> |
| 74 <option value="8">mate is unmapped</option> | 81 <option value="8">mate is unmapped</option> |