Mercurial > repos > devteam > picard
comparison picard_macros.xml @ 32:f9242e01365a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author | iuc |
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date | Mon, 25 Sep 2023 08:32:17 +0000 |
parents | 6f9c0884a3e7 |
children | 3f254c5ced1d |
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31:585027e65f3b | 32:f9242e01365a |
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1 <macros> | 1 <macros> |
2 <token name="@TMPDIR_OPTION@"> | |
3 `if [ -n "\$TMPDIR" ] ; then echo 'TMP_DIR=\$TMPDIR' ; else if [ -n "\$TEMP" ] ; then echo 'TMP_DIR=\$TEMP' ; fi ; fi`</token> | |
4 <xml name="VS"> | 2 <xml name="VS"> |
5 <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> | 3 <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> |
6 <option value="LENIENT" selected="True">Lenient</option> | 4 <option value="LENIENT" selected="True">Lenient</option> |
7 <option value="SILENT">Silent</option> | 5 <option value="SILENT">Silent</option> |
8 <option value="STRICT">Strict</option> | 6 <option value="STRICT">Strict</option> |
34 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier)) | 32 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier)) |
35 ln -f -s '$inputFile' '$escaped_element_identifier' && | 33 ln -f -s '$inputFile' '$escaped_element_identifier' && |
36 ]]></token> | 34 ]]></token> |
37 | 35 |
38 <token name="@java_options@"><![CDATA[ | 36 <token name="@java_options@"><![CDATA[ |
39 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && | 37 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} && |
40 export _JAVA_OPTIONS && | 38 export _JAVA_OPTIONS && |
41 ]]></token> | 39 ]]></token> |
42 | 40 |
43 <token name="@handle_reference_source@"><![CDATA[ | 41 <token name="@handle_reference_source@"><![CDATA[ |
44 #if str( $reference_source.reference_source_selector ) == "history": | 42 #if str( $reference_source.reference_source_selector ) == "history": |