changeset 1:e3862632706d draft

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

--- a/annotate.xml	Mon Jan 25 17:50:47 2021 +0000
+++ b/annotate.xml	Fri Apr 16 21:32:14 2021 +0000
@@ -4,6 +4,8 @@
     <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[
@@ -175,6 +177,7 @@
                     <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">
@@ -227,7 +230,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- #5 sfg, custom -->
+        <!-- #6 sfg, custom -->
         <test expect_num_outputs="3">
             <param name="input" value="input.vcf"/>
             <conditional name="type_cond">
@@ -245,6 +248,7 @@
                     <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">
@@ -276,14 +280,14 @@
 
 **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>`_
+- 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
+- Anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID) 
+- Query (TABULAR.GZ) with query SVs matched to annotation IDs
 
 .. class:: infomark
 

--- a/macros.xml	Mon Jan 25 17:50:47 2021 +0000
+++ b/macros.xml	Fri Apr 16 21:32:14 2021 +0000
@@ -1,7 +1,17 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.0.7</token>
+    <token name="@TOOL_VERSION@">0.0.8</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="edam_topics">
+        <edam_topics>
+            <edam_topic>topic_3175</edam_topic>
+        </edam_topics>
+    </xml>
+    <xml name="edam_operations">
+        <edam_operations>
+            <edam_operation>operation_3197</edam_operation>
+        </edam_operations>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">sansa</requirement>
@@ -32,6 +42,8 @@
                 <option value="exon">exon</option>
             </param>
             <param argument="--distance" type="integer" min="0" value="1000" label="Set maximum distance" help="0: overlapping features only"/>
+            <param argument="--contained" type="boolean" truevalue="-c" falsevalue="" label="Report contained genes?" help="Useful for CNVs
+            but potentially long list of genes."/>
         </section>
     </xml>
     <xml name="s">
@@ -47,4 +59,4 @@
             <param argument="--nomatch" type="boolean" truevalue="-m" falsevalue="" label="Report SVs without match in database?"/>
         </section>
     </xml>
-</macros>
+</macros>
\ No newline at end of file