Mercurial > repos > iuc > snpsift
diff snpSift_annotate.xml @ 2:bf8c1526871b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author | iuc |
---|---|
date | Mon, 05 Dec 2016 12:11:18 -0500 |
parents | 98708b88af9f |
children | 20c7d583fec1 |
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--- a/snpSift_annotate.xml Tue Jun 07 10:04:09 2016 -0400 +++ b/snpSift_annotate.xml Mon Dec 05 12:11:18 2016 -0500 @@ -1,6 +1,6 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.1"> <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) --> <macros> @@ -10,33 +10,33 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd + @CONDA_SNPSIFT_JAR_PATH@ && + java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" $annotate_cmd #if $annotate.id : -id #elif str($annotate.info_ids).strip() != '' : -info "$annotate.info_ids" - #end if - -q "$dbSnp" "$input" > "$output" + #end if + -q "$dbSnp" "$input" > "$output" ]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> - <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" + <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> <conditional name="annotate"> <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> <when value="id"/> <when value="info"> - <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" - help="list is a comma separated list of fields. When blank, all INFO fields are included"> + <param name="info_ids" type="text" value="" label="Limit INFO annotation to these INFO IDs" help="List is a comma separated list of fields. When blank, all INFO fields are included"> <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> </when> </conditional> - <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> + <param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Allow unsorted VCF files"> <help> This option will load the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files). - Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). + Otherwise, both the database and the input VCF files should be sorted by position (Chromosome sort order can differ between files). </help> </param> </inputs>