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comparison snpEff.xml @ 5:92b80578fa22 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:25 -0400
parents 114f423f99c0
children 9ec1cb6f760d
comparison
equal deleted inserted replaced
4:b86c907031ad 5:92b80578fa22
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
7 <command> 8 <command>
8 <![CDATA[ 9 <![CDATA[
9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
10 -c \$SNPEFF_JAR_PATH/snpEff.config 11 -c \$SNPEFF_JAR_PATH/snpEff.config
11 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
12 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
13 -spliceSiteSize $spliceSiteSize 14 -spliceSiteSize $spliceSiteSize
14 #end if 15 #end if
15 #if $filterIn and $filterIn.__str__ != 'no_filter': 16 #if $filterIn and $filterIn.__str__ != 'no_filter':
16 $filterIn 17 $filterIn
17 #end if 18 #end if
18 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': 19 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
19 $filterHomHet 20 $filterHomHet
20 #end if 21 #end if
21 #if $annotations and $annotations.__str__ != '': 22 #if $annotations and $annotations.__str__ != '':
22 #echo " " 23 #echo " "
23 #echo ' '.join($annotations.__str__.split(',')) 24 #echo ' '.join($annotations.__str__.split(','))
24 #end if 25 #end if
31 #end if 32 #end if
32 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 33 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
33 -interval $intervals 34 -interval $intervals
34 #end if 35 #end if
35 #if $statsFile: 36 #if $statsFile:
36 -stats $statsFile 37 -stats $statsFile
37 #end if 38 #end if
38 #if $offset.__str__ != 'default': 39 #if $offset.__str__ != 'default':
39 ${offset} 40 ${offset}
40 #end if 41 #end if
41 #if $chr.__str__.strip() != '': 42 #if $chr.__str__.strip() != '':
42 -chr "$chr" 43 -chr "$chr"
43 #end if 44 #end if
44 $noLog 45 $noLog
45 #if $snpDb.genomeSrc == 'cached': 46 #if $snpDb.genomeSrc == 'cached':
46 -dataDir ${snpDb.genomeVersion.fields.path} 47 -dataDir ${snpDb.genomeVersion.fields.path}
47 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 48 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
48 #echo " " 49 #echo " "
49 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 50 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
61 #end if 62 #end if
62 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 63 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
63 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 64 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
64 #end if 65 #end if
65 ${snpDb.snpeff_db.metadata.genome_version} 66 ${snpDb.snpeff_db.metadata.genome_version}
66 #else 67 #else
67 -download 68 -download
68 $snpDb.genome_version 69 $snpDb.genome_version
69 #end if 70 #end if
70 $input > $snpeff_output ; 71 $input > $snpeff_output ;
71 #if $statsFile: 72 #if $statsFile:
250 </data> 251 </data>
251 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> 252 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
252 <filter>generate_stats == True</filter> 253 <filter>generate_stats == True</filter>
253 </data> 254 </data>
254 </outputs> 255 </outputs>
255 <expand macro="stdio" />
256 <tests> 256 <tests>
257 <!-- Check that an effect was added in out VCF --> 257 <!-- Check that an effect was added in out VCF -->
258 <!-- Check for a HTML header indicating that this was successful --> 258 <!-- Check for a HTML header indicating that this was successful -->
259 <!-- 259 <!--
260 <output name="statsFile"> 260 <output name="statsFile">
261 <assert_contents> 261 <assert_contents>
262 <has_text text="SnpEff: Variant analysis" /> 262 <has_text text="SnpEff: Variant analysis" />
263 </assert_contents> 263 </assert_contents>
264 </output> 264 </output>
265 --> 265 -->
266 <!-- Setting filterOut throws exception in twilltestcase.py 266 <!-- Setting filterOut throws exception in twilltestcase.py
267 <test> 267 <test>
268 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 268 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
269 <param name="inputFormat" value="vcf"/> 269 <param name="inputFormat" value="vcf"/>
270 <param name="outputFormat" value="vcf"/> 270 <param name="outputFormat" value="vcf"/>
279 <assert_contents> 279 <assert_contents>
280 <has_text text="EFF=" /> 280 <has_text text="EFF=" />
281 </assert_contents> 281 </assert_contents>
282 </output> 282 </output>
283 </test> 283 </test>
284 --> 284 -->
285 285
286 <test> 286 <test>
287 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> 287 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
288 <param name="inputFormat" value="vcf"/> 288 <param name="inputFormat" value="vcf"/>
289 <param name="outputFormat" value="vcf"/> 289 <param name="outputFormat" value="vcf"/>