comparison snpSift_dbnsfp.xml @ 2:c838e7136a40 draft

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

1:13191d4914f7

<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">
    <description>Add Annotations from dbNSFP or similar annotation DBs</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        java -Xmx6G -jar "\$SNPEFF_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

    </inputs>
    <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><![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:

  2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.


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

@CITATION_SECTION@

]]>
    </help>
    <expand macro="citations">
        <citation type="doi">DOI: 10.1002/humu.21517</citation>
        <citation type="doi">DOI: 10.1002/humu.22376</citation>

2:c838e7136a40

<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
    <description>Add Annotations from dbNSFP or 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

    </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:

  2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.


@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>