changeset 0:d04d5afec2e0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:44:53 -0400
parents
children 8e5feca6a518
files README.rst crossmap_bam.xml dump2/.gitignore dump2/out.bam.bam dump2/out.bam.unmap.bam dump2/out2.bam dump2/out2.sorted.bam dump2/out2.sorted.bam.bai dump2/out2.sorted.bam.bam dump2/output2.bam dump2/output2.unmap.bam macros.xml test-data/aToB.over.chain 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_a.unmap.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_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_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_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
diffstat 36 files changed, 886 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Sep 26 05:44:53 2017 -0400
@@ -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_bam.xml	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,136 @@
+<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
+    <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[
+        #if $input_file.extension == "bam":
+            #set $input_file = "input.sam"
+            samtools view -h '${seq_source.input}' > '${input_file}' &&
+        #else:
+            #set $input_file = "input.bam"
+            ln -s '${seq_source.input}' '${input_file}'
+        #end if
+
+        CrossMap.py
+            bam
+
+            "$chain_source.input_chain"
+            $optional_tags
+
+            -m $insert_size
+            -s $insert_size_stdev
+            -t $insert_size_fold
+
+            '${input_file}'
+            '${output}'
+
+            && samtools sort "${output}.sam" > '${output}'
+            && samtools sort "${output}.unmap.sam" > '${output_unmapped}'
+    ]]></command>
+
+    <inputs>
+        <conditional name="seq_source">
+            <expand macro="source" />
+            <when value="cached">
+                <param type="data" format="bam" name="input" label="BAM file">
+                    <validator type="unspecified_build"/>
+                    <!-- Gives error in tests
+                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
+                    -->
+                </param>
+                <param name="input_chain" type="select" label="Lift Over To">
+                    <options from_file="liftOver.loc">
+                        <column name="name" index="1"/>
+                        <column name="value" index="2"/>
+                        <column name="dbkey" index="0"/>
+                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" format="bam" name="input" label="BAM/SAM file"/>
+                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+        <expand macro="chain" />
+        <param name="optional_tags" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM/SAM Headers" argument="-a"/>
+
+        <param name="insert_size" type="float" value="200.0" label="Insert size" argument="-m" help="Average insert size of pair-end sequencing (bp) [default=200.0]"/>
+        <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev" argument="-s" help="Stanadard deviation of insert size. [default=30.0]"/>
+        <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange" argument="-t" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]"/>
+</inputs>
+
+    <outputs>
+        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
+        <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
+    </outputs>
+
+    <tests>
+    <!-- BAM/SAM -->
+        <test>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+
+            <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
+            <output name="output_unmapped" file="test_bam_01_output_a.unmap.bam" compare="diff" lines_diff="8"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_GENERAL@
+
+SAM / BAM
+---------
+
+    CrossMap updates chromosomes, genome coordinates, header sections, and all
+    SAM flags accordingly. The program version (of CrossMap) is inserted into the
+    header section, along with the names of the original BAM file and the chain
+    file. For pair-end sequencing, insert size is also recalculated.
+
+
+    **Optional tags**
+
+    Q
+      QC. QC failed.
+
+    N
+      Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
+
+    M
+      Multiple mapped. Alignment can be liftover to multiple places.
+
+    U
+      Unique mapped. Alignment can be liftover to only 1 place.
+
+    **Tags for pair-end sequencing include:**
+
+    QF = QC failed
+    NN = both read1 and read2 unmapped
+    NU = read1 unmapped, read2 unique mapped
+    NM = read1 unmapped, multiple mapped
+    UN = read1 uniquely mapped, read2 unmap
+    UU = both read1 and read2 uniquely mapped
+    UM = read1 uniquely mapped, read2 multiple mapped
+    MN = read1 multiple mapped, read2 unmapped
+    MU = read1 multiple mapped, read2 unique mapped
+    MM = both read1 and read2 multiple mapped
+
+    **Tags for single-end sequencing include**
+
+    QF = QC failed
+    SN = unmaped
+    SM = multiple mapped
+    SU = uniquely mapped
+
+See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details
+]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dump2/.gitignore	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,1 @@
+*
Binary file dump2/out2.bam has changed
Binary file dump2/out2.sorted.bam has changed
Binary file dump2/out2.sorted.bam.bai has changed
Binary file dump2/out2.sorted.bam.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
+            <requirement type="package" version="0.2.2">crossmap</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@WRAPPER_VERSION@">0.2.2</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>CrossMap.py 2&gt;&amp;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_file="liftOver.loc">
+                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
+                        <column name="name" index="1"/><!-- species/build 'to' -->
+                        <column name="value" index="2"/><!-- path of chain file -->
+                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="source">
+        <param name="index_source" type="select" label="Source for Input Data">
+            <option value="cached">Local data (in galaxy)</option>
+            <option value="history">From History</option>
+        </param>
+    </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
+++ b/test-data/aToB.over.chain	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,498 @@
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+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
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	Tue Sep 26 05:44:53 2017 -0400
@@ -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_a.unmap.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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,5 @@
+chr1	100	10000	Fail
+chr2	100	10000	Fail
+chr3	100	10000	Fail
+chr4	8941700 8947200	Fail
+chr5	1	100000000	Fail
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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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_vcf_01.fasta	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -0,0 +1,5 @@
+##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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_wig_01_input_a.wig	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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	Tue Sep 26 05:44:53 2017 -0400
@@ -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>