annotate gemini_dump.xml @ 2:a32c298053e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Extract data from the Gemini DB</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">dump</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            $report
            $header
            $tfam

            "${ infile }"
            > "${ outfile }"
]]>
    </command>
    <inputs>
        <expand macro="infile" />

        <param name="report" type="select" label="The information to be reported" help="(-t)">
            <option value="--variants">All rows/columns from the variants table (--variants)</option>
            <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
            <option value="--samples">All rows/columns from the samples table (--samples)</option>
        </param>
        <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
        <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
            <param name="header" value="True" />
            <param name="report" value="--genotypes" />
            <output name="outfile" file="gemini_dump_result.tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Reports information in a Gemini database.

**Setting examples**


**--samples**

GEMINI output with setting --samples (and --header)::

 sample_id   family_id   name   paternal_id   maternal_id   sex   phenotype
 1           1           1_dad  0             0             -1    1
 2           1           1_mom  0             0             -1    1
 3           1           1_kid  1_dad         1_mom         -1    2
 4           2           2_dad  0             0             -1    1
 5           2           2_mom  0             0             -1    2
 6           2           2_kid  2_dad         2_mom         -1    2
 7           3           3_dad  0             0             -1    2
 8           3           3_mom  0             0             -1    -9
 9           3           3_kid  3_dad         3_mom         -1    2


**--variants**

GEMINI output with setting --variants (and --header)::

 chrom     start     end      vcf_id     variant_id     anno_id     ref     alt     qual           filter     type     sub_type    ... 
 chr10     1142207   1142208  .          1              4           T       C       3404.30004883  .          snp      ts          ...
 chr10     48003991  48003992 .          3              1           C       T       1047.86999512  .          snp      ts          ...

 
**--genotypes**

GEMINI output with setting --genotypes (and --header)::

 chrom  start     end        ref  alt     type    sub_type    aaf              in_dbsnp     gene       sample      genotype
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      1_dad       T/T
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      1_mom       T/T
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      1_kid       T/C
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      2_dad       T/T
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      2_mom       T/C
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      2_kid       T/C
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      3_dad       T/C
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      3_mom       T/T
 chr10  1142207   1142208    T    C       snp     ts          0.277777777778   1            WDR37      3_kid       T/C
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     1_dad       C/C
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     1_mom       C/C
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     1_kid       C/T
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     2_dad       C/C
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     2_mom       C/T
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     2_kid       C/T
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     3_dad       C/T
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     3_mom       C/C
 chr10  48003991  48003992   C    T       snp     ts          0.277777777778   1            ASAH2C     3_kid       C/T
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     1_dad       C/C
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     1_mom       C/C
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     1_kid       C/T
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     2_dad       C/C
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     2_mom       C/T
 chr10  48004991  48004992   C    T       snp     ts          0.277777777778   0            ASAH2C     2_kid       C/T


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