Mercurial > repos > iuc > snpsift
changeset 6:2b3e65a4252f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e
| author | iuc |
|---|---|
| date | Wed, 16 Jan 2019 15:35:26 -0500 |
| parents | 09d6806c609e |
| children | 2e497a770bca |
| files | snpSift_annotate.xml test-data/db_test_1.vcf |
| diffstat | 2 files changed, 44 insertions(+), 16 deletions(-) [+] |
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--- a/snpSift_annotate.xml Wed Apr 18 07:28:51 2018 -0400 +++ b/snpSift_annotate.xml Wed Jan 16 15:35:26 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy0"> +<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy1"> <description>SNPs from dbSnp</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) @@ -11,10 +11,9 @@ <expand macro="version_command" /> <command><![CDATA[ SnpSift -Xmx8G annotate -#if $annotate.id == 'id': - -id -#elif str($annotate.info_ids).strip() != '': - -info "$annotate.info_ids" +${annotate.no_info} +#if str($annotate.info_ids).strip(): + -info '$annotate.info_ids' #end if -q '$dbSnp' '$input' > '$output' ]]></command> @@ -23,14 +22,16 @@ <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> <conditional name="annotate"> - <param name="id" type="select" label="Fields to annotate"> - <option value="id">Only annotate ID field (no INFO fields will be added)</option> - <option value="info">Add also INFO fields</option> + <param name="no_info" type="select" label="Fields to annotate"> + <option value="-noInfo">Only annotate ID field (no INFO fields will be added)</option> + <option value="">Add also INFO fields</option> </param> - <when value="id"/> - <when value="info"> + <when value="-noInfo"> + <param name="info_ids" type="hidden" value="" /> + </when> + <when value=""> <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included"> - <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> + <validator type="regex" message="IDs separated by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> </when> </conditional> @@ -42,10 +43,37 @@ <test> <param name="input" ftype="vcf" value="annotate_1.vcf"/> <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> - <param name="id" value="id"/> + <conditional name="annotate"> + <param name="no_info" value=""/> + </conditional> <output name="output"> <assert_contents> - <has_text text="rs76166080" /> + <has_line_matching expression="1	872687	rs76166080	C	G	.	.	.+;.+" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="vcf" value="annotate_1.vcf"/> + <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> + <conditional name="annotate"> + <param name="no_info" value=""/> + <param name="info_ids" value="dbSNPBuildID" /> + </conditional> + <output name="output"> + <assert_contents> + <has_line_matching expression="1	872687	rs76166080	C	G	.	.	dbSNPBuildID=137" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="vcf" value="annotate_1.vcf"/> + <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/> + <conditional name="annotate"> + <param name="no_info" value="-noInfo"/> + </conditional> + <output name="output"> + <assert_contents> + <has_line line="1	872687	rs76166080	C	G	.	.	." /> </assert_contents> </output> </test> @@ -53,7 +81,7 @@ <help><![CDATA[ This is typically used to annotate IDs from dbSnp. -Annotatating only the ID field from dbSnp137.vcf :: +Annotating only the ID field from dbSnp137.vcf :: Input VCF: CHROM POS ID REF ALT QUAL FILTER INFO @@ -67,7 +95,7 @@ 22 16346045 rs56234788 T C 0.0 FAIL NS=244 22 16350245 rs2905295 C A 0.0 FAIL NS=192 -Annotatating both the ID and INFO fields from dbSnp137.vcf :: +Annotating both the ID and INFO fields from dbSnp137.vcf :: Input VCF: #CHROM POS ID REF ALT QUAL FILTER INFO