Mercurial > repos > iuc > snpsift_dbnsfp

comparison snpSift_dbnsfp.xml @ 2:c838e7136a40 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:13 -0500
parents 13191d4914f7
children 4e21e4f2bc48
comparison
equal deleted inserted replaced
1:13191d4914f7 2:c838e7136a40
1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
2 <description>Add Annotations from dbNSFP or similar annotation DBs</description> 2 <description>Add Annotations from dbNSFP or similar annotation DBs</description>
3 <macros> 3 <macros>
4 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v 10 @CONDA_SNPSIFT_JAR_PATH@ &&
11 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v
11 #if $db.dbsrc == 'cached': 12 #if $db.dbsrc == 'cached':
12 -db "$db.dbnsfp" 13 -db "$db.dbnsfp"
13 #if $db.annotations and str($db.annotations) != '': 14 #if $db.annotations and str($db.annotations) != '':
14 -f "$db.annotations" 15 -f "$db.annotations"
15 #end if 16 #end if
58 </inputs> 59 </inputs>
59 <outputs> 60 <outputs>
60 <data format="vcf" name="output" /> 61 <data format="vcf" name="output" />
61 </outputs> 62 </outputs>
62 <tests> 63 <tests>
64 <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
65 is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
66 when this tool is run and annotation metadata is not available
67 until after the conversion is completed.
63 <test> 68 <test>
64 <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/> 69 <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
65 <param name="dbsrc" value="history"/> 70 <param name="dbsrc" value="history"/>
66 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" /> 71 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
67 <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/> 72 <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
68 <output name="output"> 73 <output name="output">
69 <assert_contents> 74 <assert_contents>
70 <has_text text="dbNSFP_SIFT_score=0.15" /> 75 <has_text text="dbNSFP_SIFT_score=0.15" />
71 </assert_contents> 76 </assert_contents>
72 </output> 77 </output>
73 </test> 78 </test> -->
74 </tests> 79 </tests>
75 <help><![CDATA[ 80 <help><![CDATA[
76 81
77 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.). 82 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
78 It contains variant annotations such as: 83 It contains variant annotations such as:
277 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**. 282 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.
278 283
279 284
280 @EXTERNAL_DOCUMENTATION@ 285 @EXTERNAL_DOCUMENTATION@
281 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP 286 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
282
283 @CITATION_SECTION@
284
285 ]]> 287 ]]>
286 </help> 288 </help>
287 <expand macro="citations"> 289 <expand macro="citations">
288 <citation type="doi">DOI: 10.1002/humu.21517</citation> 290 <citation type="doi">DOI: 10.1002/humu.21517</citation>
289 <citation type="doi">DOI: 10.1002/humu.22376</citation> 291 <citation type="doi">DOI: 10.1002/humu.22376</citation>