Mercurial > repos > nml > pangolin

changeset 3:24c005390360 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 8a1337fc6ef2b8b3f2f82ebdf3ee8dbb6e3ff1ed"
author nml
date Mon, 11 May 2020 19:23:31 -0400
parents c897e502c084
children 35566aadcfc7
files macros.xml pangolin.xml test-data/lineage_report.tsv
diffstat 3 files changed, 23 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon May 04 16:40:54 2020 -0400
+++ b/macros.xml	Mon May 11 19:23:31 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">1.1.5</token>
+    <token name="@VERSION@">1.1.11</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">pangolin</requirement>
--- a/pangolin.xml	Mon May 04 16:40:54 2020 -0400
+++ b/pangolin.xml	Mon May 11 19:23:31 2020 -0400
@@ -41,14 +41,28 @@
     <tests>
         <test>
             <param name="input1" value="test_seqs.fasta" />
-            <output name="lineage_report" value="lineage_report.tsv" />
+            <output name="lineage_report" >
+                <assert_contents>
+                    <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
+                    <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
+                    <has_text text="This_seq_is_too_short" />
+                    <has_text text="lineage" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input1" value="test_seqs.fasta" />
             <section name="additional">
                 <param name="write_tree" value="true" />
             </section>
-            <output name="lineage_report" value="lineage_report.tsv" />
+            <output name="lineage_report" >
+                <assert_contents>
+                    <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
+                    <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
+                    <has_text text="This_seq_is_too_short" />
+                    <has_text text="lineage" />
+                </assert_contents>
+            </output>
             <output_collection name="pangolin_trees" type="list">
                 <element name="USA_NY-NYUMC7_2020_EPI_ISL_418192__USA_New_York_Manhattan_2020-03-16" ftype="iqtree">
                     <assert_contents>
--- a/test-data/lineage_report.tsv	Mon May 04 16:40:54 2020 -0400
+++ b/test-data/lineage_report.tsv	Mon May 11 19:23:31 2020 -0400
@@ -1,7 +1,7 @@
 taxon	lineage	SH-alrt	UFbootstrap	lineages_version	status	note
-Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17	B	100	100	2020-04-27	passed_qc	
-USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16	B.1	100	100	2020-04-27	passed_qc	
-This_seq_has_no_seq	None	0	0	2020-04-27	fail	seq_len:0
-This_seq_is_too_short	None	0	0	2020-04-27	fail	seq_len:2997
-This_seq_has_lots_of_Ns	None	0	0	2020-04-27	fail	N_content:0.98
-This_seq_is_literally_just_N	None	0	0	2020-04-27	fail	N_content:1.0
+Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17	B	100	100	2020-05-07	passed_qc	
+USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16	B.1	100	100	2020-05-07	passed_qc	
+This_seq_has_no_seq	None	0	0	2020-05-07	fail	seq_len:0
+This_seq_is_too_short	None	0	0	2020-05-07	fail	seq_len:2997
+This_seq_has_lots_of_Ns	None	0	0	2020-05-07	fail	N_content:0.98
+This_seq_is_literally_just_N	None	0	0	2020-05-07	fail	N_content:1.0