annotate gemini_db_info.xml @ 4:f3cc64057b4e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>List the gemini database tables and columns</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">db_info</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            "${ infile }" | tr -s ' ' '\t'
            > "${ outfile }"
]]>
    </command>
    <inputs>
        <expand macro="infile" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="table_name&#009;column_name&#009;type.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote.
If you can’t recall the name of particular column, just use the db_info tool.
It will report all of the tables and all of the columns / types in each table::

 table_name          column_name                   type
 variants            chrom                         text
 variants            start                         integer
 variants            end                           integer
 variants            variant_id                    integer
 variants            anno_id                       integer
 variants            ref                           text
 variants            alt                           text
 variants            qual                          float
 variants            filter                        text
 variants            type                          text
 variants            sub_type                      text
 variants            gts                           blob
 variants            gt_types                      blob
 variants            gt_phases                     blob
 variants            gt_depths                     blob
 variants            call_rate                     float
 variants            in_dbsnp                      bool
 variants            rs_ids                        text
 variants            in_omim                       bool
 variants            clin_sigs                     text
 variants            cyto_band                     text
 variants            rmsk                          text
 variants            in_cpg_island                 bool
 variants            in_segdup                     bool
 variants            is_conserved                  bool
 variants            num_hom_ref                   integer
 variants            num_het                       integer
 variants            num_hom_alt                   integer
 variants            num_unknown                   integer
 variants            aaf                           float
 variants            hwe                           float
 variants            inbreeding_coeff              float
 variants            pi                            float
 variants            recomb_rate                   float
 variants            gene                          text
 variants            transcript                    text
 variants            is_exonic                     bool
 variants            is_coding                     bool
 variants            is_lof                        bool
 variants            exon                          text
 variants            codon_change                  text
 variants            aa_change                     text
 ...                 ...                           ... 

For more columns see https://gemini.readthedocs.org/en/latest/content/tools.html#db-info-list-the-gemini-database-tables-and-columns

    ]]></help>
    <expand macro="citations"/>
</tool>