Mercurial > repos > iuc > strelka_germline

changeset 1:19481653a22f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 8e20575721a463931a4b9fbbe905d90cc2863575"
author iuc
date Tue, 02 Mar 2021 17:46:39 +0000
parents 1fbe84e8a740
children
files strelka_germline.xml
diffstat 1 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/strelka_germline.xml	Wed Jan 27 14:48:23 2021 +0000
+++ b/strelka_germline.xml	Tue Mar 02 17:46:39 2021 +0000
@@ -179,7 +179,7 @@
             </section>
             <output name="out_variants" ftype="vcf_bgzip" file="variants_test2.vcf" decompress="true" compare="diff" lines_diff="8" />
         </test>
-        <!-- #3; input bam, no defaults -->
+        <!-- #3; input bam, no defaults (note without s_e_e (genome) output seem not deterministic -->
         <test expect_num_outputs="2">
             <param name="bam" value="sample1.cram,sample2.cram"/>
             <conditional name="ref_cond">
@@ -208,12 +208,14 @@
                 </assert_contents>
             </output>
             <output_collection name="out_genome" type="list" count="2">
-                <element name="S1" ftype="vcf_bgzip">
+                <!-- assertions are applied to compressed output (even with decomress true)
+                https://github.com/galaxyproject/galaxy/issues/11521
+                <element name="S1" ftype="vcf_bgzip" decompress="true">
                     <assert_contents>
-                        <has_n_lines n="219"/>
-                        <has_line_matching expression="demo20&#009;4101&#009;.+"/>
+                        <has_n_lines n="139"/>
+                        <has_line_matching expression="demo20&#009;.+"/>
                     </assert_contents>
-                </element>
+                </element> -->
             </output_collection>
         </test>
     </tests>