Mercurial > repos > avowinkel > gatk

comparison analyze_covariates.xml @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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-1:000000000000 0:b80ff7f43ad1
1 <macros>
2 <xml name="AnalyzeCovariatesParameters" tokens="tag">
3
4 <!-- BQSR in main config -->
5
6 <param name="afterReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR second-pass report file" help="-after,&#8209;&#8209;afterReportFile &amp;lt;afterReportFile&amp;gt;" />
7
8 <param name="beforeReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR first-pass report file" help="-before,&#8209;&#8209;beforeReportFile &amp;lt;beforeReportFile&amp;gt;" />
9
10 </xml>
11
12 <xml name="AnalyzeCovariatesOutput">
13 <data format="pdf" name="ac_plotsReportFile" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (PDF Recalibration Report)">
14 <yield />
15 </data>
16 </xml>
17
18 <template name="AnalyzeCovariatesPreprocessing">
19 <![CDATA[
20 ]]>
21 </template>
22
23 <template name="AnalyzeCovariatesOptions">
24 <![CDATA[
25 --plotsReportFile ${ac_plotsReportFile}
26
27 #if str($analysis_type.afterReportFile)
28 --afterReportFile $analysis_type.afterReportFile
29 #end if
30 #if str($analysis_type.beforeReportFile)
31 --beforeReportFile $analysis_type.beforeReportFile
32 #end if
33 ]]>
34 </template>
35 </macros>
36
37