# HG changeset patch
# User nml
# Date 1588361597 14400
# Node ID b91b3923656ed9f695029f67c6f6c1883c9eae1f
# Parent  f612c8391bd86510a781e5778a12759decb9de5f
"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 216d09e3d63a6ab4245df78c111ca97d4e0b14de"

diff -r f612c8391bd8 -r b91b3923656e pangolin.xml
--- a/pangolin.xml	Fri May 01 11:30:48 2020 -0400
+++ b/pangolin.xml	Fri May 01 15:33:17 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="pangolon" name="Pangolin" version="@VERSION@+galaxy0">
+<tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0">
     <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description>
     <macros>
         <import>macros.xml</import>
@@ -6,8 +6,9 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length'
+pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' &&
 
+sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
     ]]></command>
     <inputs>
         <param name="input1" type="data" format="fasta"
@@ -25,12 +26,12 @@
         </section>
     </inputs>
     <outputs>
-        <data format="csv" from_work_dir="lineage_report.csv" name="lineage_report" label="${input1.name}_lineage_report" />
+        <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
     </outputs>
     <tests>
         <test>
             <param name="input1" value="test_seqs.fasta" />
-            <output name="lineage_report" value="lineage_report.csv" />
+            <output name="lineage_report" value="lineage_report.tsv" />
         </test>
     </tests>
     <help><![CDATA[
diff -r f612c8391bd8 -r b91b3923656e test-data/lineage_report.csv
--- a/test-data/lineage_report.csv	Fri May 01 11:30:48 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-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
diff -r f612c8391bd8 -r b91b3923656e test-data/lineage_report.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lineage_report.tsv	Fri May 01 15:33:17 2020 -0400
@@ -0,0 +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