comparison snpSift_dbnsfp.xml @ 1:1f4ee04c0841 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp_generic/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

0:0624d484adba

<tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="4.0.0">
    <description>Add Annotations from dbNSFP and similar annotation DBs</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">
            <param name="dbsrc" type="select" label="dbNSFP ">

                  </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <expand macro="stdio" />
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/>
            <param name="dbsrc" value="history"/>
            <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
            <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/>
            <output name="output">
                <assert_contents>
                    <has_text text="dbNSFP_SIFT_score=0.15" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
It contains variant annotations such as:

  ESP6500_AA_AF
    Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
  ESP6500_EA_AF
    Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
  FATHMM_pred
    If a FATHMM_score is <=-1.5 (or rankscore <=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
  FATHMM_rankscore
    FATHMMori scores were ranked among all FATHMMori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMori scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1
  FATHMM_score
    FATHMM default score (FATHMMori)
  fold-degenerate

  LR_score
    Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1
  LRT_Omega
    Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
  LRT_converted_rankscore
    LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682
  LRT_pred
    LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
  LRT_score
    The original LRT two-sided p-value (LRTori), ranges from 0 to 1
  MutationAssessor_pred

  Reliability_index
    Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for RadialSVM and LR. Ranges from 1 to 10. As RadialSVM and LR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions
  SIFT_converted_rankscore
    SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.02654 to 0.87932
  SIFT_pred
    If SIFTori is smaller than 0.05 (rankscore>0.55) the corresponding non-synonymous SNP is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";"
  SIFT_score
    SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";"
  SiPhy_29way_logOdds
    SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
  SiPhy_29way_pi

    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 procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:
http://snpeff.sourceforge.net/SnpSift.html#dbNSFP

A couple dbNSFP databases are prebuilt for SnpSift at: 
http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/




**Uploading Your Own Annotations for any Genome**

The website for dbNSFP databases releases is:  

The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.


@EXTERNAL_DOCUMENTATION@
	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP

@CITATION_SECTION@


    </help>
</tool>

1:1f4ee04c0841

<tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
    <description>Add Annotations from dbNSFP and similar annotation DBs</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPSIFT_JAR_PATH@ &&
        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v
        #if $db.dbsrc == 'cached':
          -db $db.dbnsfp 
          #if $db.annotations and str($db.annotations) != '':
            -f "$db.annotations"
          #end if
        #else:
          -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
          #if $db.annotations and str($db.annotations) != '':
            -f "$db.annotations"
          #end if
        #end if
        "$input" > "$output"
        2> tmp.err && grep -v file tmp.err
]]>
    </command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
        <conditional name="db">
            <param name="dbsrc" type="select" label="dbNSFP ">

                  </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
    <tests>
        <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
             is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
             when this tool is run and annotation metadata is not available
             until after the conversion is completed.
        <test>
            <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
            <param name="dbsrc" value="history"/>
            <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
            <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
            <output name="output">
                <assert_contents>
                    <has_text text="dbNSFP_SIFT_score=0.15" />
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[

The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
It contains variant annotations such as:

  ESP6500_AA_AF
    Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
  ESP6500_EA_AF
    Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
  FATHMM_pred
    If a FATHMM_score is <=-1.5 (or rankscore <=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
  FATHMM_rankscore
    FATHMMori scores were ranked among all FATHMMori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMori scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1
  FATHMM_score
    FATHMM default score (FATHMMori)
  fold-degenerate

  LR_score
    Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1
  LRT_Omega
    Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
  LRT_converted_rankscore
    LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682
  LRT_pred
    LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
  LRT_score
    The original LRT two-sided p-value (LRTori), ranges from 0 to 1
  MutationAssessor_pred

  Reliability_index
    Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for RadialSVM and LR. Ranges from 1 to 10. As RadialSVM and LR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions
  SIFT_converted_rankscore
    SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.02654 to 0.87932
  SIFT_pred
    If SIFTori is smaller than 0.05 (rankscore>0.55) the corresponding non-synonymous SNP is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";"
  SIFT_score
    SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";"
  SiPhy_29way_logOdds
    SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
  SiPhy_29way_pi

    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 procedure for preparing the dbNSFP data for use in SnpSift dbnsfp and a couple of prebuilt dbNSFP databases are available at:
http://snpeff.sourceforge.net/SnpSift.html#dbNSFP


**Uploading Your Own Annotations for any Genome**

The website for dbNSFP databases releases is:  

The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.


@EXTERNAL_DOCUMENTATION@
	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
]]>
    </help>
    <expand macro="citations">
        <citation type="doi">DOI: 10.1002/humu.21517</citation>
        <citation type="doi">DOI: 10.1002/humu.22376</citation>
        <citation type="doi">DOI: 10.1002/humu.22932</citation>
        <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
        <citation type="doi">doi: 10.1093/nar/gku1206</citation>
        <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
    </expand>
</tool>