add initial odgi tools

tools/odgi/.shed.yml

@@ -0,0 +1,16 @@
+owner: iuc
+long_description: |
+  Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. 
+  odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/
+homepage_url: https://github.com/vgteam/odgi
+type: unrestricted
+categories:
+ - Sequence Analysis
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the odgi tool: {{ tool_name }}"
+suite:
+  name: "suite_odgi"
+  description: "odgi - optimized dynamic genome/graph implementation"
+  type: repository_suite_definition

tools/odgi/build.xml

@@ -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>

tools/odgi/macros.xml

@@ -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>

tools/odgi/test-data/note5.gfa

@@ -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+	*,*,*,*,*,*,*,*,*

tools/odgi/test-data/t.gfa

@@ -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

tools/odgi/vis.xml

@@ -0,0 +1,57 @@
+<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@">
+    <description>variation graph visualizations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi viz
+-i '$input'
+--out='$output'
+-x $width
+-y $height
+#if str($path_height)
+    --path-height=$path_height
+#end if
+#if str($path_x_padding)
+    --path-x-padding=$path_x_padding
+#end if
+$path_per_row
+#if str($link_path_pieces):
+    --link-path-pieces=$link_path_pieces
+#end if
+--threads=\${GALAXY_SLOTS:-1}
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="odgi" label="odgi input file" />
+
+        <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" />
+        <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" />
+
+        <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" />
+        <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" />
+        <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue=""
+            label="Display a single path per row rather than packing them" />
+
+        <param argument="--link-path-pieces" type="float" optional="true"
+            label="Show thin links of this relative width to connect path pieces" />
+    </inputs>
+    <outputs>
+        <data name="output" format="png" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="note5_out.og" />
+            <param name="width" value="4000" />
+            <param name="height" value="500" />
+            <output name="output" file="note5.png" ftype="png" />
+        </test>
+    </tests>
+    <help><![CDATA[
+optimized dynamic genome/graph implementation (odgi)
+----------------------------------------------------
+
+variation graph visualizations (viz)
+    ]]></help>
+    <expand macro="citations" />
+</tool>