Mercurial > repos > iuc > crossmap_region
changeset 0:8635b6b8a8f2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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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 +++ b/test-data/aToB.over.chain Thu Jul 15 16:19:33 2021 +0000 @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 +1242 28 28 +574 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/aToB.over.chain Thu Jul 15 16:19:33 2021 +0000 @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 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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
--- /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 *
--- /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
--- /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
--- /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>