# HG changeset patch
# User iuc
# Date 1586421401 14400
# Node ID a347dad1f30559563fce5ce515d29c6ad8a7a5e8

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"

diff -r 000000000000 -r a347dad1f305 deconstruct.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deconstruct.xml	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,82 @@
+<tool id="vg_deconstruct" name="vg deconstruct" 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[
+ln -s '$infile' ./infile.${infile.ext} &&
+
+vg deconstruct
+#if $path:
+    --path '${','.join([$p for $p in $path])}'
+#end if
+#if $path_prefix
+    --path-prefix '${','.join([$p for $p in $path_prefix])}'
+#end if
+#if $alt_prefix
+    --alt-prefix '${','.join([$p for $p in $alt_prefix])}'
+#end if
+#if $snarls:
+    --snarls '$snarls'
+#end if
+$path_traversals  ## -e
+--threads=\${GALAXY_SLOTS:-1}
+./infile.${infile.ext}
+
+> '$output'
+
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="xg,odgi" label="Graph files" />
+        <param argument="--path" type="text" value="" label="A reference path to deconstruct against"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true"
+            help="from `vg snarls` to avoid recomputing" />
+
+        <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false"
+            label="Only consider traversals that correspond to paths in the grpah" />
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="hla.xg" />
+            <param name="path" value="gi|568815592:29791752-29792749" />
+            <param name="path_traversals" value="true" />
+            <output name="output" file="hla_variants.vcf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+variation graph (vg) deconstruct module
+-----------------------------------
+
+Creates VCF records for Snarls present in a graph (relative to a chosen reference path).
+
+    ]]></help>
+    <expand macro="citations">
+    </expand>
+</tool>
diff -r 000000000000 -r a347dad1f305 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">vg</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">1.23.0</token>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r a347dad1f305 test-data/hla.vg
Binary file test-data/hla.vg has changed
diff -r 000000000000 -r a347dad1f305 test-data/hla.xg
Binary file test-data/hla.xg has changed
diff -r 000000000000 -r a347dad1f305 test-data/hla_variants.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hla_variants.vcf	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,21 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=gi|568815592:29791752-29792749,length=998>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	gi|157734152:29563108-29564082	gi|528476637:29761569-29762543	gi|568815454:1057585-1058559	gi|568815529:1275535-1276509	gi|568815551:1054737-1055734	gi|568815561:1054328-1055325	gi|568815564:1054403-1055400	gi|568815567:1054737-1055711	gi|568815569:1097903-1098900
+gi|568815592:29791752-29792749	92	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	105	.	C	T	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	151	.	CAG	C	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	160	.	A	G	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	222	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	283	.	C	G	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	295	.	TT	CC	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	348	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	357	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	395	.	T	C	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	468	.	T	C	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	583	.	G	C	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	621	.	G	T	23	.	.	GT	0	1	0	0	0	0	0	1	0
+gi|568815592:29791752-29792749	660	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	824	.	CGCGGGCGCCGTGGATGGAGCA	C	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	982	.	G	A	23	.	.	GT	1	1	1	1	0	0	0	1	0
+gi|568815592:29791752-29792749	995	.	C	T	23	.	.	GT	1	1	1	1	0	0	0	1	0
diff -r 000000000000 -r a347dad1f305 test-data/snarls.pb
Binary file test-data/snarls.pb has changed
diff -r 000000000000 -r a347dad1f305 test-data/x.gfa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/x.gfa	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,513 @@
+H	VN:Z:1.0
+S	56	ATTAGCCATGTGACTTTGAACAAGTTAGTTAA
+S	35	A
+S	110	TCATTGTCAAC
+S	60	T
+S	30	ACGTTTGACAATCTATCAC
+S	6	TTG
+S	67	T
+S	215	A
+S	73	A
+S	182	CTGCTCTCTT
+S	164	G
+S	115	ACATTAGGA
+S	153	T
+S	112	ACAGTCAACGCTCAATACAAGG
+S	185	TTGTCAGATC
+S	64	A
+S	186	G
+S	90	GAGGAAAGCCTCTGACAACTGGT
+S	139	GGGCAC
+S	4	T
+S	13	A
+S	86	C
+S	168	A
+S	207	CAAA
+S	104	TCCTTG
+S	183	A
+S	52	A
+S	177	T
+S	12	ATAT
+S	179	TGTCCAGGAATGAACC
+S	75	A
+S	23	T
+S	111	A
+S	41	TGGAGCCA
+S	43	G
+S	11	T
+S	68	GGAGAT
+S	171	G
+S	69	C
+S	82	G
+S	85	G
+S	130	TTGTGT
+S	119	G
+S	125	T
+S	39	C
+S	77	A
+S	126	G
+S	108	C
+S	71	AT
+S	66	C
+S	103	C
+S	156	C
+S	59	G
+S	172	CTGCTCTTTCCCTCAATTGTTCATTTGTCT
+S	208	T
+S	2	A
+S	10	A
+S	27	CTTTGATTTATTTGAAGT
+S	26	T
+S	211	GG
+S	124	TAAGACCCAGAGGGCTCACCCAGAGTCGAG
+S	144	T
+S	127	CTCAAGGACAGCTCTCC
+S	116	A
+S	100	T
+S	79	TTTGCTGTGAAGATTAAATTAGGTGATGCTTG
+S	200	C
+S	20	TGCTATGTGTAACTAGTAATGGTAATGGATAT
+S	81	T
+S	195	A
+S	141	T
+S	187	A
+S	213	A
+S	135	T
+S	9	AAATTTTCTGGAGTTCTAT
+S	189	A
+S	138	T
+S	109	T
+S	161	T
+S	107	GGCTCTTCTGGCTT
+S	46	T
+S	57	TCTCTCTGAACTTCAGTT
+S	152	GCTCTCCTTGTCCCTCC
+S	170	C
+S	88	C
+S	129	T
+S	209	G
+S	120	CTCTGCTCACCG
+S	78	G
+S	133	CAGAGTGTATACGA
+S	72	G
+S	24	TT
+S	8	G
+S	184	C
+S	37	A
+S	1	CAAATAAG
+S	137	TAACTCTGTTC
+S	22	C
+S	83	A
+S	154	C
+S	190	C
+S	201	T
+S	99	C
+S	121	C
+S	206	C
+S	14	T
+S	33	AGGGGTAATGTGGGGAA
+S	40	T
+S	113	A
+S	174	T
+S	165	A
+S	142	GGTGAAAGA
+S	5	C
+S	55	T
+S	114	G
+S	123	GATCTTCAAGTTTGAAAATTGCATCTCAAATC
+S	32	T
+S	136	G
+S	117	T
+S	45	C
+S	145	AACAGAGGAAATGCC
+S	197	T
+S	196	AGGGC
+S	210	CTACCCAGGCCATTTTAAGTTTCCTGT
+S	151	A
+S	54	G
+S	63	C
+S	191	TTCTCATCCCTCCT
+S	91	G
+S	62	ATT
+S	205	TACTCCACAT
+S	158	GATCTCTTCACT
+S	150	T
+S	176	C
+S	122	T
+S	58	C
+S	199	T
+S	28	A
+S	173	C
+S	148	GGCTTTTTATCAGAACATGTTTCCAAGCTTAT
+S	188	G
+S	92	A
+S	36	TGGAAAGAATAC
+S	98	TA
+S	204	C
+S	118	TGGCAGTAGCTCAGAGATCT
+S	162	C
+S	84	AAGCT
+S	7	A
+S	25	C
+S	203	G
+S	95	TTACTG
+S	76	G
+S	34	G
+S	50	TCCTCACTTTGCC
+S	93	A
+S	18	TCCTGG
+S	194	G
+S	147	T
+S	42	T
+S	87	AGGGAATAGTGCCTGGCAT
+S	132	C
+S	140	C
+S	157	A
+S	167	G
+S	169	GAA
+S	202	TAA
+S	16	G
+S	180	G
+S	160	GCCT
+S	19	T
+S	49	A
+S	44	ACAAATCTGGGT
+S	31	C
+S	146	G
+S	74	CTACTGACAGCAGA
+S	106	A
+S	61	A
+S	29	G
+S	94	G
+S	212	ACTAAGGACAAAGGTGCGGGGAGAT
+S	102	GAAACATTTGGCTATTGACCTCTTTC
+S	128	C
+S	159	G
+S	70	G
+S	21	GTTGGGCTT
+S	193	C
+S	38	AAGAT
+S	163	TTATCTTTACTGTTACC
+S	131	T
+S	192	T
+S	101	TTACTATGAATCCTCACCTTCCTTGACTTCTT
+S	105	G
+S	17	T
+S	53	CA
+S	47	CAA
+S	175	A
+S	166	AATCTTTCC
+S	89	A
+S	214	G
+S	198	C
+S	3	G
+S	80	TGA
+S	96	C
+S	51	G
+S	178	A
+S	149	CCCTTTTCCC
+S	155	A
+S	181	A
+S	143	A
+S	48	G
+S	15	CCAACTCTCTGG
+S	65	TCTCTAATA
+S	97	T
+S	134	A
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diff -r 000000000000 -r a347dad1f305 test-data/x.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/x.json	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,1 @@
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Binary file test-data/x.vg has changed