comparison snpSift_dbnsfp.xml @ 114:fc8a3e1e7880 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 344140b8df53b8b7024618bb04594607a045c03a

113:f915cd331e53

<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
    <description>Add Annotations from dbNSFP</description>
    <expand macro="requirements" />
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <command>
        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
        #if $db.dbsrc == 'cached' :
          -db $db.dbnsfp 
          #if $db.annotations and $db.annotations.__str__ != '':
            -f "$db.annotations"
          #end if
        #else :
          -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
          #if $db.annotations and $db.annotations.__str__ != '':
            -f "$db.annotations"
          #end if
        #end if          
        $input > $output  
        2> tmp.err &amp;&amp; grep -v file tmp.err
    </command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
        <conditional name="db">

                  </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <expand macro="stdio" />
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <test>

    Uniprot ID number. Multiple entries separated by ";"
  UniSNP_ids
    rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...


The website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 genome builds. 

However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::

	- The first line of the file must be column headers that name the annotations.  
	- The first 4 columns are required and must be::
		1. chromosome 
		2. position in chromosome
		3. reference base
		4. alternate base

For example:

114:fc8a3e1e7880

<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
    <description>Add Annotations from dbNSFP</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
        #if $db.dbsrc == 'cached' :
          -db $db.dbnsfp
          #if $db.annotations and $db.annotations.__str__ != '':
            -f "$db.annotations"
          #end if
        #else :
          -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
          #if $db.annotations and $db.annotations.__str__ != '':
            -f "$db.annotations"
          #end if
        #end if
        $input > $output
        2> tmp.err &amp;&amp; grep -v file tmp.err
    </command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
        <conditional name="db">

                  </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <test>

    Uniprot ID number. Multiple entries separated by ";"
  UniSNP_ids
    rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...


The website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 genome builds.

However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::

	- The first line of the file must be column headers that name the annotations.
	- The first 4 columns are required and must be::
		1. chromosome
		2. position in chromosome
		3. reference base
		4. alternate base

For example: