# HG changeset patch
# User fubar
# Date 1726891298 0
# Node ID 794aecef8327af6d9256575634303b4557f90d48
# Parent  c4b77883c0a7b93735c8328767ca8a44e004b6a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7b6920fd88a86cdb48dc4af2c6be77161eb85699-dirty

diff -r c4b77883c0a7 -r 794aecef8327 __pycache__/jbrowse2.cpython-312.pyc
Binary file __pycache__/jbrowse2.cpython-312.pyc has changed
diff -r c4b77883c0a7 -r 794aecef8327 foo
Binary file foo has changed
diff -r c4b77883c0a7 -r 794aecef8327 foo.tbi
Binary file foo.tbi has changed
diff -r c4b77883c0a7 -r 794aecef8327 jbrowse2.py
--- a/jbrowse2.py	Mon Sep 02 09:56:39 2024 +0000
+++ b/jbrowse2.py	Sat Sep 21 04:01:38 2024 +0000
@@ -411,7 +411,7 @@
             []
         )  # for default session - these are read as first line of the assembly .fai
         self.giURL = GALAXY_INFRASTRUCTURE_URL
-        self.outdir = outdir
+        self.outdir = os.path.abspath(outdir)
         self.jbrowse2path = jbrowse2path
         os.makedirs(self.outdir, exist_ok=True)
         self.genome_names = []
@@ -444,7 +444,7 @@
             log.debug(command)
         p = subprocess.Popen(
             command,
-            cwd=self.get_cwd(cwd),
+            cwd=self.outdir,
             shell=True,
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
@@ -1440,8 +1440,6 @@
                 )
             session_views.append(view_json)
         session_name = default_data.get("session_name", "New session")
-        for key, value in mapped_chars.items():
-            session_name = session_name.replace(value, key)
         session_json["name"] = session_name
 
         if "views" not in session_json:
diff -r c4b77883c0a7 -r 794aecef8327 jbrowse2.xml
--- a/jbrowse2.xml	Mon Sep 02 09:56:39 2024 +0000
+++ b/jbrowse2.xml	Sat Sep 21 04:01:38 2024 +0000
@@ -639,11 +639,9 @@
                 <param name="zipOut" value="true"/>
                 <param name="session_name" value="New test session"/>
             </section>
-            <!-- use the following line to generate a ZIP file to inspect it -->
-            <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"-->
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="637" delta="10"/>
+                    <has_archive_member path=".*" n="678" delta="10"/>
                     <has_archive_member path="index.html"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
@@ -696,11 +694,9 @@
                 <param name="session_name" value="Collection test"/>
                 <param name="ucol|formcoll" value="collect"/>
             </section>
-            <!-- use the following line to generate a ZIP file to inspect it -->
-            <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"-->
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <has_archive_member path=".*" n="611" delta="10"/>
+                    <has_archive_member path=".*" n="652" delta="10"/>
                     <has_archive_member path="index.html"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
@@ -1117,8 +1113,7 @@
             </section>
             <output name="output" ftype="zip">
                 <assert_contents>
-                    <!-- roughly 590 files in an archive -->
-                    <has_archive_member path=".*" n="608" delta="30"/>
+                    <has_archive_member path=".*" n="649" delta="30"/>
                     <has_archive_member path="index.html"/>
                     <has_archive_member path="manifest.json">
                         <has_text text="favicon.ico"/>
diff -r c4b77883c0a7 -r 794aecef8327 macros.xml
--- a/macros.xml	Mon Sep 02 09:56:39 2024 +0000
+++ b/macros.xml	Sat Sep 21 04:01:38 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.14.0</token>
+    <token name="@TOOL_VERSION@">2.15.4</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>
@@ -15,11 +15,11 @@
             <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
             <requirement type="package" version="1.82">biopython</requirement>
             <requirement type="package" version="0.7.1">bcbio-gff</requirement>
-            <requirement type="package" version="1.19">samtools</requirement>
+            <requirement type="package" version="1.21">samtools</requirement>
             <requirement type="package" version="6.0.1">pyyaml</requirement>
             <requirement type="package" version="1.11">tabix</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
-            <requirement type="package" version="0.0.12-0">hictk</requirement>
+            <requirement type="package" version="1.0.0">hictk</requirement>
             <requirement type="package" version="3.0">zip</requirement>
             <yield/>
         </requirements>
diff -r c4b77883c0a7 -r 794aecef8327 test-data/vcf/merlin.vcf.2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcf/merlin.vcf.2	Sat Sep 21 04:01:38 2024 +0000
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+Merlin	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+Merlin	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+Merlin	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+Merlin	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+Merlin	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff -r c4b77883c0a7 -r 794aecef8327 test-data/vcf/merlinold.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcf/merlinold.vcf	Sat Sep 21 04:01:38 2024 +0000
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number	of	Samples	With	Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total	Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele	Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral	Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP	membership,	build	129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2	membership">
+##FILTER=<ID=q10,Description="Quality	below	10">
+##FILTER=<ID=s50,Description="Less	than	50%	of	samples	have	data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype	Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read	Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype	Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+Merlin	61	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+Merlin	122	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+Merlin	488	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+Merlin	549	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+Merlin	1098	microsat1		G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3