changeset 0:8635b6b8a8f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:19:33 +0000
parents
children eb66d7a04bf8
files README.rst crossmap_region.xml macros.xml test-data/aToB.over.chain test-data/cached_locally/aToB.over.chain test-data/cached_locally/liftOver.loc test-data/test_bam_01_input_a.bam test-data/test_bam_01_input_a.sam test-data/test_bam_01_output_a.bam test-data/test_bam_01_output_b.bam test-data/test_bam_01_output_b.unmap.bam test-data/test_bed_01_input_a.bed test-data/test_bed_01_output_a__all.bed test-data/test_bed_01_output_a__only-matches.bed test-data/test_bed_01_output_a__only_fails.bed test-data/test_bed_02_input_a.bed test-data/test_bed_02_output_a__all.bed test-data/test_bed_02_output_a__only-matches.bed test-data/test_bed_02_output_a__only_fails.bed test-data/test_bigwig_01_input_a.bw test-data/test_bigwig_01_output_a.bw test-data/test_bigwig_01_output_a.sorted.bgr test-data/test_gff_01_input_a.gtf test-data/test_gff_01_output_a__all.gtf test-data/test_gff_01_output_a__only-matches.gtf test-data/test_region.bed test-data/test_vcf_01.fasta test-data/test_vcf_01.over.chain test-data/test_vcf_01_input.vcf test-data/test_vcf_01_output.vcf.unmap test-data/test_wig_01_input_a.wig test-data/test_wig_01_output_a.bw test-data/test_wig_01_output_a.sorted.bgr tool-data/all_fasta.loc.sample tool-data/liftOver.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 35 files changed, 1371 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,7 @@
+CrossMap wrapper for Galaxy
+===========================
+
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crossmap_region.xml	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,79 @@
+<tool id="crossmap_region" name="CrossMap region" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>Convert genome coordinates or annotation files between genome assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+CrossMap.py region
+    '${chain_source.input_chain}'
+    '${input}'
+    --ratio $ratio
+    '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="bed" label="BED file"
+               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
+        <expand macro="chain" />
+        <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
+            <param name="index_source" value="history"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <output name="output" file="test_region.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+CrossMap region
+---------------
+
+Unlike the "CrossMap bed" function which splits big genomic regions, "CrossMap region" tries to convert the big genomic region as a whole.
+
+BED
+---
+
+BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
+BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
+
+A BED (Browser Extensible Data) file is a tab-delimited text file
+describing genome regions or gene annotations. It is the standard file
+format used by UCSC. It consists of one line per feature, each containing
+3-12 columns. CrossMap converts BED files with less than 12 columns to a
+different assembly by updating the chromosome and genome coordinates only;
+all other columns remain unchanged. Regions from old assembly mapping to
+multiple locations to the new assembly will be split. For 12-columns BED
+files, all columns will be updated accordingly except the 4th column (name
+of bed line), 5th column (score value) and 9th column (RGB value describing
+the display color). 12-column BED files usually define multiple blocks (eg.
+exon); if any of the exons fails to map to a new assembly, the whole BED
+line is skipped.
+
+Notes:
+
+1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
+   column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
+   any). All other columns will keep AS-IS.
+2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
+3. Lines will less than 3 columns will be skipped.
+4. 2nd-column and 3-column must be integer, otherwise skipped.
+5. “+” strand is assumed if no strand information was found.
+6. For standard BED format (12 columns). If any of the defined exon blocks
+   cannot be uniquely mapped to target assembly, the whole entry will be
+   skipped.
+7. If input region cannot be consecutively mapped target assembly, it will be split.
+8. \*.unmap file contains regions that cannot be unambiguously converted.
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.5.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="stdio">
+        <stdio>
+            <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
+            <regex match=".*" source="both" level="log"/>
+            <exit_code range="1:"/>
+        </stdio>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[
+CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
+        ]]></version_command>
+    </xml>
+    <xml name="chain">
+        <conditional name="chain_source">
+            <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                <option value="cached">Local data (in galaxy)</option>
+                <option value="history">From History</option>
+            </param>
+            <when value="cached">
+                <param name="input_chain" type="select" label="Lift Over To">
+                    <options from_data_table="liftOver">
+                        <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input_chain" type="data" format="txt" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@HELP_GENERAL@">
+CrossMap
+--------
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
+    </token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+1022394	50000	50000
+281532	289973	50000
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+1556908	150000	50000
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+17265625	50000	50000
+11394365	50000	50000
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+174886
+
+chain 22466185064 chr2 243199373 + 10000 243102476 chr2 242951149 + 0 242751149 1
+1201236	0	1
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+26	1	1
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+4029	0	9
+967	4547	1000
+420	27	0
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+2458	17	17
+4595	4	0
+3531	14	14
+3954	51129	50000
+1426129	160449	100025
+11087286	0	3
+773	103977	50000
+1576	0	1
+240	0	1
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+2851	10	10
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+4783388	35000	25000
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+7799848	851	851
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+7529698	72396	0
+1891551	294073	150000
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+9017	0	266
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+290931	1273578	1000000
+731068	3000000	3000000
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+702023	72796	150000
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+172366	0	281526
+40517	0	406
+58864	1	2
+1843	0	2
+14994	0	1
+12992	2	0
+2571146	1	0
+35688061	108224	100000
+29671719	1	0
+39665349	1	0
+14876089	64197	20000
+401	0	3
+1831	1	1
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+654	11	1
+127	0	28
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+1139	0	8
+138	144	813
+71	1	0
+385638	1	1
+219	1	1
+51	7	7
+54	15205	15205
+54	7	7
+51	1	1
+110	1	1
+5198249	0	1
+115	80	0
+60	40	0
+80	100	20
+442	1	1
+35	1	1
+119	9	129
+14	0	40
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+85	0	40
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+1194	12	14
+1773	0	5
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+2422	21	22
+2315	0	1
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+970	6	6
+7234	4	0
+1228	1	0
+1233	8	1
+4207	1	1
+41	1	1
+1715	50	50
+1532	0	2
+1714	2	0
+2299	2	0
+2143	1	1
+18	1	1
+917	1	0
+1082	1	1
+49	1	1
+9098	0	4
+5529	0	1
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+894	6	0
+1440	1	1
+2095	2	0
+4179	18	13
+1785	0	1
+1674	0	6
+1217	32348	33000
+287	17	23
+40	173	0
+20	161	0
+13	66	0
+12	71	1
+12548	30000	30000
+952154	41011	25000
+1914	1	0
+225	1	1
+57	1	1
+2910	0	1
+471	1	0
+1956	1	1
+43	1	1
+991	0	92
+2863	3	0
+1838	306	0
+1006	30	0
+206	1	1
+27	0	3
+221	17	17
+1525	8	0
+413	1	1
+32	2	2
+1573	12	12
+2258676
+
+chain 18404394637 chr3 198022430 + 60000 197962430 chr3 199501827 + 35000 199446827 3
+13552792	0	1
+585083	0	1
+2092	1	2
+71	0	1
+31067262	0	1
+90	1	0
+5628461	0	15
+788	1	0
+3676	0	2
+35	1	1
+4682	1	0
+1295	0	5
+437	53	42
+326	0	2
+3309	1	1
+40	1	1
+998	0	3
+3584	5	0
+930	5	7
+845	1	1
+28	2	1
+303	0	1
+507	0	5
+5088	1	0
+2185	10046	10048
+949	4	4
+35	1	1
+2874	0	1
+6717	0	1
+2823	1	0
+703	0	4
+5143	1	0
+2490	10	10
+162	7	7
+6308	0	15
+15177535	152352	260003
+2532	1	0
+1633	2	2
+24207544	3000000	4400000
+60453436	0	4
+40076813	20999	20000
+8195	1	1
+44	1	1
+1408	1	1
+33	1	1
+172	3	4
+25	1	1
+538	13	13
+173	1	1
+27	1	1
+636	1	1
+28	1	1
+470	3	3
+112	1	1
+375	1	1
+26	26	0
+115	78	0
+52	23	0
+104	26	0
+15	231	0
+56	1	1
+20	1	1
+815	16	16
+484	1	1
+49	18	0
+509	4	3
+23	1	1
+391	1	1
+44	1	1
+1278	0	4
+32	1	1
+263	4	0
+27	1	1
+2416	0	2
+3184	43	43
+1150	13	13
+736	1	1
+47	1	1
+1416	1	1
+20	1	1
+1020	1	1
+25	1	1
+482	5	0
+716	1	0
+1697	1	1
+29	1	1
+1270261	23108	27000
+40930	1	0
+17455	1	1
+28	4	4
+43	0	491
+1679	1	1
+33	7	5
+29	1	3
+54863	53	16
+7653	2	2
+29	2	2
+15	0	30
+180	0	75
+215	45	0
+360	915	0
+6188	96	0
+17	288	0
+1388	1	1
+37	1	1
+7956	0	1
+374	0	1
+2442058
+
+chain 310844 chr4 191154276 + 9241835 9252105 chr4 191273063 + 8941714 8947231 850
+2726	14	14
+243	9	9
+78	4	4
+157	213	211
+265	85	85
+524	4751	0
+379	283	283
+539
+
+chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837
+59	380	365
+9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/liftOver.loc	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,32 @@
+#This is a sample file distributed with Galaxy that is used by the
+#liftOver tools.  The liftOver.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+#
+#So, for example, if you had the chain file to convert from anoCar1 to galGal3
+#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
+#then the liftOver.loc entry would look like this:
+#
+#<FromSpecies>  <ToSpecies> <PathToChainFile>
+#<dbkey>        <name>      <value>
+#
+#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#
+#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
+#contain all of your "chain" files (e.g.):
+#
+#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
+#...etc...
+#
+#Your liftOver.loc file should include an entry per line for each build you can
+#convert.  For example:
+#
+#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+#...etc...
+
+hg18	hg19	${__HERE__}/aToB.over.chain
Binary file test-data/test_bam_01_input_a.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bam_01_input_a.sam	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,27 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:1000051
+@SQ	SN:chr2	LN:1000051
+@SQ	SN:chr3	LN:1000051
+@SQ	SN:chr4	LN:9250051
+@PG	ID:-	VN:1.0.0	CL:cmatrix
+@CO	Test data for CrossMap bam
+read_001	0	chr1	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_002	0	chr2	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_003	0	chr3	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_004	0	chr4	9200000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_005	0	chr4	8940000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_006	0	chr1	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_007	0	chr2	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_008	0	chr3	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_009	0	chr4	9250000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_010	0	chr4	9000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_011	16	chr1	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_012	16	chr2	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_013	16	chr3	100000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_014	16	chr4	9200000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_015	16	chr4	8940000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_016	16	chr1	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_017	16	chr2	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_018	16	chr3	1000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_019	16	chr4	9250000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
+read_020	16	chr4	9000000	60	50M	*	0	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	*
Binary file test-data/test_bam_01_output_a.bam has changed
Binary file test-data/test_bam_01_output_b.bam has changed
Binary file test-data/test_bam_01_output_b.unmap.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_01_input_a.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	100000	1000000
+chr2	100000	1000000
+chr3	100000	1000000
+chr4	9200000	9250000
+chr4	8940000	9000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_01_output_a__all.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,14 @@
+chr1	100000	1000000	(split.1:chr1:100000:177417:+)	chr1	89863	167280
+chr1	100000	1000000	(split.2:chr1:227417:267719:+)	chr1	217280	257582
+chr1	100000	1000000	(split.3:chr1:317719:471368:+)	chr1	307582	461231
+chr1	100000	1000000	(split.4:chr1:521368:1000000:+)	chr1	511231	989863
+chr2	100000	1000000	->	chr2	90000	990000
+chr3	100000	1000000	->	chr3	75000	975000
+chr4	9200000	9250000	(split.1:chr4:9241835:9244561:+)	chr4	8941714	8944440
+chr4	9200000	9250000	(split.2:chr4:9244575:9244818:+)	chr4	8944454	8944697
+chr4	9200000	9250000	(split.3:chr4:9244827:9244905:+)	chr4	8944706	8944784
+chr4	9200000	9250000	(split.4:chr4:9244909:9245066:+)	chr4	8944788	8944945
+chr4	9200000	9250000	(split.5:chr4:9245279:9245544:+)	chr4	8945156	8945421
+chr4	9200000	9250000	(split.6:chr4:9245629:9246153:+)	chr4	8945506	8946030
+chr4	8940000	9000000	(split.1:chr4:8982741:8982800:+)	chr10	15069810	15069869
+chr4	8940000	9000000	(split.2:chr4:8983180:8983189:+)	chr10	15069436	15069445
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_01_output_a__only-matches.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,14 @@
+chr1	89863	167280
+chr1	217280	257582
+chr1	307582	461231
+chr1	511231	989863
+chr2	90000	990000
+chr3	75000	975000
+chr4	8941714	8944440
+chr4	8944454	8944697
+chr4	8944706	8944784
+chr4	8944788	8944945
+chr4	8945156	8945421
+chr4	8945506	8946030
+chr10	15069810	15069869
+chr10	15069436	15069445
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_02_input_a.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	100	10000
+chr2	100	10000
+chr3	100	10000
+chr4	8941700 8947200 
+chr5	1	100000000
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
Binary file test-data/test_bigwig_01_input_a.bw has changed
Binary file test-data/test_bigwig_01_output_a.bw has changed
Binary file test-data/test_bigwig_01_output_a.sorted.bgr has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_gff_01_input_a.gtf	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1"; 
+chr2	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1"; 
+chr3	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1"; 
+chr4	CrossMap_test_data	CDS	9200000	9250000	0.000000	-	0	gene_id "TEST_GENE_1"; 
+chr5	CrossMap_test_data	CDS	8940000	9000000	0.000000	-	0	gene_id "TEST_GENE_1"; 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_gff_01_output_a__all.gtf	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,5 @@
+chr1	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1";	fail (multpile match to target assembly)
+chr2	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1";	->	chr2	CrossMap_test_data	CDS	90000	990000	0.000000	-	0	gene_id "TEST_GENE_1";
+chr3	CrossMap_test_data	CDS	100000	1000000	0.000000	-	0	gene_id "TEST_GENE_1";	->	chr3	CrossMap_test_data	CDS	75000	975000	0.000000	-	0	gene_id "TEST_GENE_1";
+chr4	CrossMap_test_data	CDS	9200000	9250000	0.000000	-	0	gene_id "TEST_GENE_1";	fail (multpile match to target assembly)
+chr5	CrossMap_test_data	CDS	8940000	9000000	0.000000	-	0	gene_id "TEST_GENE_1";	fail (no match to target assembly)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_gff_01_output_a__only-matches.gtf	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,2 @@
+chr2	CrossMap_test_data	CDS	90000	990000	0.000000	-	0	gene_id "TEST_GENE_1";
+chr3	CrossMap_test_data	CDS	75000	975000	0.000000	-	0	gene_id "TEST_GENE_1";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_region.bed	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,2 @@
+chr2	90000	990000	map_ratio=1.0000
+chr3	75000	975000	map_ratio=1.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf_01.fasta	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,10 @@
+>chr1
+CAAAAAAGCAGTTGACAGTTGTTCGGGCTTGTTACGCATCTTAAGATCGAATAAGGAGAGAGGGTCTAAACG
+AGGCGCACCCCGCCTATGGGTGATCGAGGTACTAGGGGTTGGTCGCAGGTCTGTATTACCGTTAGCGGTGCA
+AGGGGATCTGATCGAGTGATTCACCTACTCATGTGGCGAGCACGCCGACGAAATACTCCTGGTCGTGTTATA
+AAGCCCTGGTTTTCCTTTCC
+>chr2
+CACAAAATGCACGTGGATGCAGGCATTTATCCAACCCACACTATTACGTTCACCAAATGTGTGGACCAACTG
+CGGGACTAGGTAAGCTTGTCCTCAATGAGCGAAATTGATATTTCTCTACCGACTTGGGGTCGACTGGACGAG
+TCAGCTGTGCAACAGCTCAGCCGGTTTCGATAAACCGAAACCTTGAATGTTTGGACTTGCGTCATGGCGAAC
+AAAGATCGTTCATGTCGCA
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf_01.over.chain	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,11 @@
+chain 4900 chr1 236 + 1 236 chr2 236 - 1 237 1
+ 9       1       0
+ 10      0       5
+ 61      4       0
+ 16      0       4
+ 42      3       0
+ 16      0       8
+ 14      1       0
+ 3       7       0
+ 48
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf_01_input.vcf	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
+##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
+1	10	rs11449	G	A	.	PASS	.	GT	0/0	0/1
+1	100 rs84825 C	C	.	PASS	.	GT:GP	0/1:.	0/1:0.03,0.97,0
+1	200 rs84823 T	G	.	PASS	.	GT:PL	./.:.	1/1:10,5,0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf_01_output.vcf.unmap	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
+##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
+1	200 rs84823 T	G	.	PASS	.	GT:PL	./.:.	1/1:10,5,0	Fail(REF==ALT)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_wig_01_input_a.wig	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,10 @@
+variableStep chrom=chr1 span=900000
+100000 110
+variableStep chrom=chr2 span=900000
+100000 220
+variableStep chrom=chr3 span=900000
+100000 330
+variableStep chrom=chr4 span=50000
+9200000 400
+variableStep chrom=chr4 span=60000
+8940000 450
Binary file test-data/test_wig_01_output_a.bw has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_wig_01_output_a.sorted.bgr	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,2 @@
+chr2	89999	989999	220.0
+chr3	74999	974999	330.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/liftOver.loc.sample	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that is used by the
+#liftOver tools.  The liftOver.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+#
+#So, for example, if you had the chain file to convert from anoCar1 to galGal3
+#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
+#then the liftOver.loc entry would look like this:
+#
+#<FromSpecies>  <ToSpecies> <PathToChainFile>
+#<dbkey>        <name>      <value>
+#
+#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#
+#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
+#contain all of your "chain" files (e.g.):
+#
+#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
+#...etc...
+#
+#Your liftOver.loc file should include an entry per line for each build you can
+#convert.  For example:
+#
+#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of all liftOver files -->
+    <table name="liftOver" comment_char="#">
+         <columns>dbkey, name, value</columns>
+        <file path="tool-data/liftOver.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Jul 15 16:19:33 2021 +0000
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" />
+    </table>
+    <!-- Locations of all liftOver files -->
+    <table name="liftOver" comment_char="#">
+        <columns>dbkey, name, value</columns>
+        <file path="${__HERE__}/test-data/cached_locally/liftOver.loc" />
+    </table>
+</tables>