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comparison picard_macros.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 6f9c0884a3e7
children 3f254c5ced1d
comparison
equal deleted inserted replaced
31:585027e65f3b 32:f9242e01365a
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":