Mercurial > repos > iuc > sansa_annotate

diff annotate.xml @ 1:b4b8e88c6ff9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
author iuc
date Fri, 16 Apr 2021 21:31:21 +0000
parents 608c3eefface
children c3877d3a230e
line wrap: on
line diff
--- a/annotate.xml	Mon Jan 25 17:49:56 2021 +0000
+++ b/annotate.xml	Fri Apr 16 21:31:21 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