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comparison picard_macros.xml @ 14:486d7500da69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:09 -0400
parents 3d8d70436d02
children a5a13ea16d17
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13:c7dd8d7946b8 14:486d7500da69
5 <option value="SILENT">Silent</option> 5 <option value="SILENT">Silent</option>
6 <option value="STRICT">Strict</option> 6 <option value="STRICT">Strict</option>
7 </param> 7 </param>
8 </xml> 8 </xml>
9 9
10 <token name="@TOOL_VERSION@">2.7.1</token> 10 <token name="@TOOL_VERSION@">2.18.2</token>
11 11
12 <xml name="requirements"> 12 <xml name="requirements">
13 <requirements> 13 <requirements>
14 <requirement type="package" version="2.7.1">picard</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">picard</requirement>
15 <yield/> 15 <yield/>
16 </requirements> 16 </requirements>
17 </xml> 17 </xml>
18 18
19 <token name="@symlink_element_identifier@"><![CDATA[ 19 <token name="@symlink_element_identifier@"><![CDATA[
23 ]]></token> 23 ]]></token>
24 24
25 <token name="@java_options@"><![CDATA[ 25 <token name="@java_options@"><![CDATA[
26 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && 26 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
27 export _JAVA_OPTIONS && 27 export _JAVA_OPTIONS &&
28 ]]></token>
29
30 <token name="@handle_reference_source@"><![CDATA[
31 #if str( $reference_source.reference_source_selector ) == "history":
32 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
33 #else:
34 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
35 #end if
28 ]]></token> 36 ]]></token>
29 37
30 <token name="@more_info@"> 38 <token name="@more_info@">
31 ------ 39 ------
32 40
94 This will be added shortly 102 This will be added shortly
95 103
96 104
97 </token> 105 </token>
98 106
107 <xml name="citations">
108 <citations>
109 <citation type="bibtex">@misc{Picard,
110 author = {Broad Institute},
111 title = {Picard},
112 publisher = {GitHub},
113 journal = { Broad Institute, GitHub repository},
114 url = {http://broadinstitute.github.io/picard/}
115 }
116 </citation>
117 </citations>
118 </xml>
119
99 120
100 </macros> 121 </macros>