--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotate.xml	Mon Jan 25 17:50:47 2021 +0000
@@ -0,0 +1,297 @@
+<?xml version="1.0"?>
+<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
+#if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
+    gzip -c '$type_cond.fg.gtf' > 'db.gtf.gz' &&
+#end if
+
+## run
+sansa annotate
+## sv annotation options
+#if $type_cond.type_sel == 's' or $type_cond.type_sel == 'sfg'
+    --db '$type_cond.s.db'
+    --bpoffset $type_cond.s.bpoffset
+    --ratio $type_cond.s.ratio
+    --strategy '$type_cond.s.strategy'
+    $type_cond.s.notype
+    $type_cond.s.nomatch
+#end if
+## feature and gene annotation options
+#if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
+    --gtf 'db.gtf.gz'
+    --id '$type_cond.fg.id'
+    --feature '$type_cond.fg.feature'
+    --distance $type_cond.fg.distance
+#end if
+## input
+'$input'
+
+## postprocessing
+2>&1 | tee -a '$out_log'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="vcf" label="Select input file"/>
+        <conditional name="type_cond">
+            <param name="type_sel" type="select" label="Select annotation mode(s)">
+                <option value="s" selected="true">SV</option>
+                <option value="fg">Feature/Gene</option>
+                <option value="sfg">SV and Feature/Gene</option>
+            </param>
+            <when value="s">
+                <expand macro="s"/>
+            </when>
+            <when value="fg">
+                <expand macro="fg"/>
+            </when>
+            <when value="sfg">
+                <expand macro="s"/>
+                <expand macro="fg"/>
+            </when>
+        </conditional>
+        <section name="oo" title="Output options" expanded="true">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+                <option value="anno" selected="true">Annotation</option>
+                <option value="log">Log</option>
+                <option value="query">Query SV</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_anno" format="bcf" from_work_dir="anno.bcf" label="${tool.name} on ${on_string}: Annotation">
+            <filter>'anno' in oo['out']</filter>
+        </data>
+        <data name="out_query" format="tabular.gz" from_work_dir="query.tsv.gz" label="${tool.name} on ${on_string}: Query SV">
+            <filter>'query' in oo['out']</filter>
+        </data>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
+            <filter>'log' in oo['out']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 s, default -->
+        <test expect_num_outputs="3">
+            <param name="input" value="input.vcf"/>
+            <conditional name="type_cond">
+                <param name="type_sel" value="s"/>
+                <section name="s">
+                    <param name="db" value="db.vcf"/>
+                </section>
+            </conditional>
+            <section name="oo">
+                <param name="out" value="anno,log,query"/>
+            </section>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="57072"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 s, custom -->
+        <test expect_num_outputs="3">
+            <param name="input" value="input.vcf"/>
+            <conditional name="type_cond">
+                <param name="type_sel" value="s"/>
+                <section name="s">
+                    <param name="db" value="db.vcf"/>
+                    <param name="bpoffset" value="51"/>
+                    <param name="ratio" value="0.79"/>
+                    <param name="strategy" value="all"/>
+                    <param name="notype" value="true"/>
+                    <param name="nomatch" value="true"/>
+                </section>
+            </conditional>
+            <section name="oo">
+                <param name="out" value="anno,log,query"/>
+            </section>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="57072"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 fg, default -->
+        <test expect_num_outputs="3">
+            <param name="input" value="input.vcf"/>
+            <conditional name="type_cond">
+                <param name="type_sel" value="fg"/>
+                <section name="fg">
+                    <param name="gtf" value="db.gtf"/>
+                </section>
+            </conditional>
+            <section name="oo">
+                <param name="out" value="anno,log,query"/>
+            </section>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="2408"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #4 fg, custom -->
+        <test expect_num_outputs="3">
+            <param name="input" value="input.vcf"/>
+            <conditional name="type_cond">
+                <param name="type_sel" value="fg"/>
+                <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>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="2408"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #5 sfg, default -->
+        <test expect_num_outputs="3">
+            <param name="input" value="input.vcf"/>
+            <conditional name="type_cond">
+                <param name="type_sel" value="sfg"/>
+                <section name="s">
+                    <param name="db" value="db.vcf"/>
+                </section>
+                <section name="fg">
+                    <param name="gtf" value="db.gtf"/>
+                </section>
+            </conditional>
+            <section name="oo">
+                <param name="out" value="anno,log,query"/>
+            </section>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="57072"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <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">
+                    <param name="db" value="db.vcf"/>
+                    <param name="bpoffset" value="51"/>
+                    <param name="ratio" value="0.79"/>
+                    <param name="strategy" value="all"/>
+                    <param name="notype" value="true"/>
+                    <param name="nomatch" value="true"/>
+                </section>
+                <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>
+            <output name="out_anno">
+                <assert_contents>
+                    <has_size value="57072"/>
+                </assert_contents>
+            </output>
+            <output name="out_query">
+                <assert_contents>
+                    <has_size value="91"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+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**
+
+More information are available on `GitHub <https://github.com/dellytools/sansa>`_.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts378</citation>
+    </citations>
+</tool>
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