comparison annotate.xml @ 1:e3862632706d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"

0:fb00426402b0

<tool id="sansa_annotate" name="sansa annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
    <description>structural variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
## file format gtf.gz is required

                <section name="fg">
                    <param name="gtf" value="db.gtf"/>
                    <param name="id" value="gene_id"/>
                    <param name="feature" value="exon"/>
                    <param name="distance" value="1001"/>
                </section>
            </conditional>
            <section name="oo">
                <param name="out" value="anno,log,query"/>
            </section>

                <assert_contents>
                    <has_text_matching expression=".+Done.+"/>
                </assert_contents>
            </output>
        </test>
        <!-- #5 sfg, custom -->
        <test expect_num_outputs="3">
            <param name="input" value="input.vcf"/>
            <conditional name="type_cond">
                <param name="type_sel" value="sfg"/>
                <section name="s">

                <section name="fg">
                    <param name="gtf" value="db.gtf"/>
                    <param name="id" value="gene_id"/>
                    <param name="feature" value="exon"/>
                    <param name="distance" value="1001"/>
                </section>
            </conditional>
            <section name="oo">
                <param name="out" value="anno,log,query"/>
            </section>

Sansa *annotate* is a structural variant (SV) annotation tool.

**Input**

- sample (VCF)
- gene annotation file (GTF/GFF2/GFF3)
- annotation database, e.g. `gnomAD-SV <https://gnomad.broadinstitute.org/>`_ or `1000 Genomes phase 3 <https://www.internationalgenome.org/phase-3-structural-variant-dataset>`_

**Output**

- anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID) 
- query (tabular.gz) with query SVs matched to annotation IDs

.. class:: infomark

**References**

1:e3862632706d

<tool id="sansa_annotate" name="sansa annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
    <description>structural variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_topics"/>
    <expand macro="edam_operations"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
## file format gtf.gz is required

                <section name="fg">
                    <param name="gtf" value="db.gtf"/>
                    <param name="id" value="gene_id"/>
                    <param name="feature" value="exon"/>
                    <param name="distance" value="1001"/>
                    <param name="contained" value="true"/>
                </section>
            </conditional>
            <section name="oo">
                <param name="out" value="anno,log,query"/>
            </section>

                <assert_contents>
                    <has_text_matching expression=".+Done.+"/>
                </assert_contents>
            </output>
        </test>
        <!-- #6 sfg, custom -->
        <test expect_num_outputs="3">
            <param name="input" value="input.vcf"/>
            <conditional name="type_cond">
                <param name="type_sel" value="sfg"/>
                <section name="s">

                <section name="fg">
                    <param name="gtf" value="db.gtf"/>
                    <param name="id" value="gene_id"/>
                    <param name="feature" value="exon"/>
                    <param name="distance" value="1001"/>
                    <param name="contained" value="true"/>
                </section>
            </conditional>
            <section name="oo">
                <param name="out" value="anno,log,query"/>
            </section>

Sansa *annotate* is a structural variant (SV) annotation tool.

**Input**

- Sample (VCF)
- Gene annotation (GTF/GFF2/GFF3)
- Annotation database, e.g. `gnomAD-SV <https://gnomad.broadinstitute.org/>`_ or `1000 Genomes phase 3 <https://www.internationalgenome.org/phase-3-structural-variant-dataset>`_

**Output**

- Anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID) 
- Query (TABULAR.GZ) with query SVs matched to annotation IDs

.. class:: infomark

**References**