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comparison picard_macros.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
16 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" /> 16 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
17 </mapping> 17 </mapping>
18 </sanitizer> 18 </sanitizer>
19 </xml> 19 </xml>
20 20
21 <token name="@TOOL_VERSION@">2.18.2</token> 21 <token name="@TOOL_VERSION@">3.1.1</token>
22 <token name="@PROFILE@">22.05</token>
22 23
23 <xml name="requirements"> 24 <xml name="requirements">
24 <requirements> 25 <requirements>
25 <requirement type="package" version="@TOOL_VERSION@">picard</requirement> 26 <requirement type="package" version="@TOOL_VERSION@">picard</requirement>
26 <yield/> 27 <yield/>
28 </xml> 29 </xml>
29 30
30 <token name="@symlink_element_identifier@"><![CDATA[ 31 <token name="@symlink_element_identifier@"><![CDATA[
31 #import re 32 #import re
32 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier)) 33 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
33 ln -f -s '$inputFile' '$escaped_element_identifier' && 34 ln -sf '$inputFile' '$escaped_element_identifier' &&
34 ]]></token> 35 ]]></token>
35 36
36 <token name="@java_options@"><![CDATA[ 37 <token name="@java_options@"><![CDATA[
37 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} && 38 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
38 export _JAVA_OPTIONS && 39 export _JAVA_OPTIONS &&
39 ]]></token> 40 ]]></token>
40 41
41 <token name="@handle_reference_source@"><![CDATA[ 42 <token name="@handle_reference_source@"><![CDATA[
42 #if str( $reference_source.reference_source_selector ) == "history": 43 #if str( $reference_source.reference_source_selector ) == "history":
43 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && 44 ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
44 #else: 45 #else:
45 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 46 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
46 #end if 47 #end if
47 ]]></token> 48 ]]></token>
48 49
110 111
111 **Dataset collections - processing large numbers of datasets at once** 112 **Dataset collections - processing large numbers of datasets at once**
112 113
113 This will be added shortly 114 This will be added shortly
114 115
115
116 </token> 116 </token>
117 117
118 <xml name="citations"> 118 <xml name="citations">
119 <citations> 119 <citations>
120 <citation type="bibtex">@misc{Picard, 120 <citation type="bibtex">@misc{Picard,
126 } 126 }
127 </citation> 127 </citation>
128 </citations> 128 </citations>
129 </xml> 129 </xml>
130 130
131
132 </macros> 131 </macros>