comparison gemini_stats.xml @ 5:86d4303cc3ca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

4:cdd90678004a

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
    <description>Compute useful variant statistics</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">stats</token>
    </macros>

    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            $stats_type

            #set $multiline_sql_expr = $gt_filter
            #set $cmdln_param = "--gt-filter"
            @MULTILN_SQL_EXPR_TO_CMDLN@

            #set $multiline_sql_expr = $summarize
            #set $cmdln_param = "--summarize"
            @MULTILN_SQL_EXPR_TO_CMDLN@

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

        <param name="stats_type" type="select" label="Studying ..." help="">
            <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
            <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
            <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
            <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
            <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
            <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
            <option value="--vars-by-sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>
            <option value="--gts-by-sample">Return the count of each genotype class observed per sample (--gts-by-sample)</option>
        </param>

        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
            <expand macro="sanitize_query" />
        </param>

        <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">
            <expand macro="sanitize_query" />
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <!-- test vars-by-sample report -->
            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
            <param name="stats_type" value="--vars-by-sample" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="sample&#009;total" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- test gts-by-sample report -->
            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
            <param name="stats_type" value="--gts-by-sample" />
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="sample&#009;num_hom_ref&#009;num_het&#009;num_hom_alt&#009;num_unknown&#009;total" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

The stats tool computes some useful variant statistics for a GEMINI database.
Like computing the transition and transversion ratios for the snps.

**Settings and examples**

--tstv-coding:
 Compute the transition/transversion ratios for the snps in the coding regions.

--tstv-noncoding:
 Compute the transition/transversion ratios for the snps in the non-coding regions.

EXAMPLE Compute the type and count of the snps; --snp-counts::

 type    count
 A->G    2
 C->T    1
 G->A    1

EXAMPLE Calculate the site frequency spectrum of the variants; --sfs::

 aaf     count
 0.125   2
 0.375   1

EXAMPLE Compute the pair-wise genetic distance between each sample; --mds::

 sample1  sample2  distance
 M10500   M10500   0.0
 M10475   M10478   1.25
 M10500   M10475   2.0
 M10500   M10478   0.5714

EXAMPLE Return a count of the types of genotypes per sample; --gts-by-sample::

 sample   num_hom_ref   num_het   num_hom_alt   num_unknown   total
 M10475   4             1         3             1             9
 M10478   2             2         4             1             9



EXAMPLE Return the total variants per sample (sum of homozygous and heterozygous variants); --vars-by-sample::

 sample  total
 M10475  4
 M10478  6

**Final solution**

--summarize:
 If none of these tools are exactly what you want, you can summarize the variants per sample of an arbitrary query using the –summarize flag. 

EXAMPLE If you wanted to know, for each sample, how many variants are on chromosome 1 that are also in dbSNP;--summarize "select * from variants where in_dbsnp=1 and chrom='chr1'":: 

 sample   total  num_het  num_hom_alt
 M10475   1      1        0
 M128215  1      1        0
 M10478   2      2        0
 M10500   2      1        1


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

5:86d4303cc3ca

<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
    <description>Compute useful variant statistics</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">stats</token>
    </macros>

    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        gemini @BINARY@
            #if str($stats.type) == "gts-stats":
                #set $multiline_sql_expr = $stats.variants.gt_filter
                #set $cmdln_param = "--gt-filter"
                @MULTILN_SQL_EXPR_TO_CMDLN@

                #if str($stats.variants.constraint).strip():
                    #set $multiline_sql_expr = "select * from variants WHERE " + str($stats.variants.constraint)
                #else:
                    #set $multiline_sql_expr = "select * from variants"
                #end if
                #set $cmdln_param = "--summarize"
                @MULTILN_SQL_EXPR_TO_CMDLN@
            #else:
                ${stats.stats_option}
            #end if
            '$infile'
            > '$outfile'
]]>
    </command>
    <inputs>
        <expand macro="infile" />

        <conditional name="stats">
            <param name="type" type="select"
            label="Select the type of statistics you are interested in" help="">
                <option value="gts-stats">Genotype counts tabulated by sample (--summarize)</option>
                <option value="snp-counts">Counts of SNPs by nucleotide change (--snp-counts)</option>
                <option value="tstv-stats">Transition / transversion statistics for the SNPs in the dataset</option>
                <option value="aaf">Alternate allele frequency spectrum of all variants (--sfs)</option>
                <option value="sample-distance">Pair-wise genetic distances between for all samples (--mds)</option>
            </param>
            <when value="snp-counts">
                <param name="stats_option" type="hidden" value="--snp-counts" />
            </when>
            <when value="aaf">
                <param name="stats_option" type="hidden" value="--sfs" />
            </when>
            <when value="sample-distance">
                <param name="stats_option" type="hidden" value="--mds" />
            </when>
            <when value="tstv-stats">
                <param name="stats_option" type="select"
                label="Calculate Ts/Tv statistics based on"
                help="Restricting the calculation to coding/noncoding regions will only produce meaningful results with preannotated variants. If you haven't annotated your variants with SnpEff or VEP before loading them into GEMINI, select All SNPs.">
                    <option value="--tstv">All SNPs (--tstv)</option>
                    <option value="--tstv-coding">SNPs in coding regions (--tstv-coding)</option>
                    <option value="--tstv-noncoding">SNPs in non-coding regions (--tstv-noncoding)</option>
                </param>
            </when>
            <when value="gts-stats">
                <param name="stats_option" type="hidden" value="" />
                <conditional name="variants">
                    <param name="keep" type="select"
                    label="Compute the genotype counts table based on"
                    help="If you select All variants the genotype counts will be produced using --summarize with the wildcard query &quot;select * from variants&quot;.">
                        <option value="all">All variants</option>
                        <option value="custom">Custom filtered variants</option>
                    </param>
                    <when value="all">
                        <param name="gt_filter" type="hidden" value="" />
                        <param name="constraint" type="hidden" value="" />
                    </when>
                    <when value="custom">
                        <param argument="--gt-filter" name="gt_filter" type="text" area="True" size="5x50"
                        label="Restrictions to apply to genotype values"
                        help="">
                            <expand macro="sanitize_query" />
                        </param>
                        <param name="constraint" type="text" area="True" size="5x50"
                        label="Additional constraints on the variants"
                        help="Enter valid constraints for the WHERE clause of a GEMINI query here. You could use, for example: chrom = 'chr1' or impact_severity = 'HIGH', to include only high-impact variants on chromosome 1 in the counts table.">
                            <expand macro="sanitize_query" />
                        </param>
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <!-- test vars-by-sample report -->
            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
            <conditional name="stats">
                <param name="type" value="tstv-stats" />
                <param name="stats_option" value="--tstv-coding" />
            </conditional>
            <output name="outfile">
                <assert_contents>
                    <!-- since the input file is not annotated
                    no variants will be considered to be in coding regions -->
                    <has_line line="ts&#009;tv&#009;ts/tv" />
                    <has_line line="0&#009;0&#009;0" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- test gts-by-sample report -->
            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
            <conditional name="stats">
                <param name="type" value="gts-stats" />
                <conditional name="variants">
                    <param name="keep" value="all" />
                </conditional>
            </conditional>
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="sample&#009;total&#009;num_het&#009;num_hom_alt&#009;num_hom_ref" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

The stats tool computes one of the following useful variant statistics for a GEMINI database:

**Genotype counts tabulated by sample**:

This mode uses the ``gemini stats --summarize`` option to produce a table with
one row per sample, which tabulates the numbers of sites, for which a given
sample shows a:

- non-reference genotype (*total* column; the sum of the *num_het* and *num_hom_alt* columns next to it)
- heterozygous genotype (*num_het* column)
- homozygous variant genotype (*num_hom_alt* column)
- homozygous reference genotype (*num_hom_ref* column)

You can choose to calculate the table based on all variants in your database,
or to filter the variants before the calculation using GEMINI genotype filter
expressions and/or WHERE clauses of GEMINI queries.

**Counts of SNPs by nucleotide change**:

This runs ``gemini stats`` with the ``--snp-count`` option. The result is a
simple table listing the number of occurences of each observed REF->ALT change
in your database, e.g.::

 type    count
 A->G    2
 C->T    1
 G->A    1

**Transition / transversion statistics**

This mode uses ``gemini stats`` with the ``--tstv``, ``--tstv-coding``, or
``--tstv-noncoding`` option to compute the transition/transversion ratios for
all SNPs, for SNPs in coding, or SNPs in non-coding regions, respectively.

The result is presented in a 1x3 table listing the number of
transitions (*ts* column), transversions (*tv* column) and the ratio of the two
(*ts/tv* column), e.g.::

 ts    tv    ts/tv
 126   39    3.2307

**Alternate allele frequency spectrum**

Runs ``gemini stats --sfs`` to produce binned alternate allele frequency counts
in a table like::

 aaf     count
 0.125   2
 0.375   1

**Pairwise genetic distances**

Runs ``gemini stats --mds`` and tabulates all pairwise genetic distance for the
samples in your database. An example could look like this::

 sample1  sample2  distance
 M10500   M10500   0.0
 M10475   M10478   1.25
 M10500   M10475   2.0
 M10500   M10478   0.5714

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