changeset 0:0acf4893bee5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build.xml	Wed Apr 08 12:12:18 2020 -0400
@@ -0,0 +1,48 @@
+<tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@">
+    <description>construct a dynamic succinct variation graph</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi build
+-g '$gfa'
+-o '$odgi_output'
+$sort
+#if $to_gfa:
+    --to-gfa > '$gfa_output'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--gfa" type="data" format="gfa1" label="Construct the graph from this GFA input file" />
+        <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false"
+            label="Topological sort the graph"
+            help="Apply generalized topological sort to the graph and set node ids to order." />
+        <param argument="--to-gfa" type="boolean" truevalue="--to-gfa" falsevalue="" checked="false"
+            label="Output additional GFA file"
+            help="" />
+    </inputs>
+    <outputs>
+        <data name="odgi_output" format="odgi" />
+        <data name="gfa_output" format="gfa1">
+            <filter>to_gfa</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gfa" value="t.gfa" />
+            <param name="sort" value="true" />
+            <param name="to_gfa" value="true" />
+            <output name="odgi_output" file="note5_out.og" />
+            <output name="gfa_output" file="note5.gfa" />
+        </test>
+    </tests>
+    <help><![CDATA[
+optimized dynamic genome/graph implementation (odgi)
+----------------------------------------------------
+
+Construct a dynamic succinct variation graph (build)
+    ]]></help>
+    <expand macro="citations">
+    </expand>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Apr 08 12:12:18 2020 -0400
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">odgi</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.3</token>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/note5.gfa	Wed Apr 08 12:12:18 2020 -0400
@@ -0,0 +1,37 @@
+H	VN:Z:1.0
+S	1	CAAATAAG
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+S	2	A
+L	2	+	4	+	0M
+L	2	+	5	+	0M
+S	3	G
+L	3	+	4	+	0M
+L	3	+	5	+	0M
+S	4	T
+L	4	+	6	+	0M
+S	5	C
+L	5	+	6	+	0M
+S	6	TTG
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+S	7	A
+L	7	+	9	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+L	9	+	10	+	0M
+L	9	+	11	+	0M
+S	10	A
+L	10	+	12	+	0M
+S	11	T
+L	11	+	12	+	0M
+S	12	ATAT
+L	12	+	13	+	0M
+L	12	+	14	+	0M
+S	13	A
+L	13	+	15	+	0M
+S	14	T
+L	14	+	15	+	0M
+S	15	CCAACTCTCTG
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*

Binary file test-data/note5.png has changed

Binary file test-data/note5_out.og has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t.gfa	Wed Apr 08 12:12:18 2020 -0400
@@ -0,0 +1,37 @@
+H	VN:Z:1.0
+S	1	CAAATAAG
+S	2	A
+S	3	G
+S	4	T
+S	5	C
+S	6	TTG
+S	7	A
+S	8	G
+S	9	AAATTTTCTGGAGTTCTAT
+S	10	A
+S	11	T
+S	12	ATAT
+S	13	A
+S	14	T
+S	15	CCAACTCTCTG
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	8M,1M,1M,3M,1M,19M,1M,4M,1M,11M
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	2	+	4	+	0M
+L	2	+	5	+	0M
+L	3	+	4	+	0M
+L	3	+	5	+	0M
+L	4	+	6	+	0M
+L	5	+	6	+	0M
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+L	7	+	9	+	0M
+L	8	+	9	+	0M
+L	9	+	10	+	0M
+L	9	+	11	+	0M
+L	10	+	12	+	0M
+L	11	+	12	+	0M
+L	12	+	13	+	0M
+L	12	+	14	+	0M
+L	13	+	15	+	0M
+L	14	+	15	+	0M