| Next changeset 1:52a9daf61566 (2017-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447 |
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README.rst crossmap_gff.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 |
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| diff -r 000000000000 -r 5773a57e91e6 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -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. |
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| diff -r 000000000000 -r 5773a57e91e6 crossmap_gff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crossmap_gff.xml Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -0,0 +1,94 @@ +<tool id="crossmap_gff" name="CrossMap GFF" 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[ + CrossMap.py gff + '${chain_source.input_chain}' + '${seq_source.input}' + + #if str($include_fails) == "True" + > + #end if + + '${output}' + ]]></command> + + <inputs> + <conditional name="seq_source"> + <expand macro="source" /> + + <when value="cached"> + <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF 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> + </when> + <when value="history"> + <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file"/> + </when> + </conditional> + <expand macro="chain" /> + + <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> + </inputs> + + <outputs> + <!-- GTF/GFF3? test... --> + <data format="gff" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + + <tests> + <!-- GFF --> + <test> + <param name="input_format" value="gff"/> + <param name="index_source" value="history"/> + <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="False"/> + + <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> + </test> + <test> + <param name="input_format" value="gff"/> + <param name="index_source" value="history"/> + <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="True"/> + + <output name="output" file="test_gff_01_output_a__all.gtf"/> + </test> + </tests> + <help><![CDATA[ +@HELP_GENERAL@ + +GFF / GTF +--------- +Your input data should be either GTF/GFF2.5 or GFF3 format. + + GFF (General Feature Format) is another plain text file used to describe + gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The + first eight fields are the same as GFF. Only chromosome and genome + coordinates are updated. The format of output is determined from the input. + + NOTE: + + - Each feature (exon, intron, UTR, etc) is processed separately and + independently, and we do NOT check if features originally belonging to + the same gene were converted into the same gene. + - If user want to liftover gene annotation files, use BED12 format. + +Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details +]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btt730</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 5773a57e91e6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -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>&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> |
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| diff -r 000000000000 -r 5773a57e91e6 test-data/aToB.over.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aToB.over.chain Tue Sep 26 05:44:21 2017 -0400 |
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| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bam_01_input_a.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bam_01_input_a.sam Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -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 * |
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| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bed_01_input_a.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_input_a.bed Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -0,0 +1,5 @@ +chr1 100000 1000000 +chr2 100000 1000000 +chr3 100000 1000000 +chr4 9200000 9250000 +chr4 8940000 9000000 |
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| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bed_01_output_a__all.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_output_a__all.bed Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bed_01_output_a__only-matches.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_output_a__only-matches.bed Tue Sep 26 05:44:21 2017 -0400 |
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| @@ -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 |
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| @@ -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 |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bed_02_output_a__all.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__all.bed Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +chr1 100 10000 Fail +chr2 100 10000 Fail +chr3 100 10000 Fail +chr4 8941700 8947200 Fail +chr5 1 100000000 Fail |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bigwig_01_input_a.bw |
| b |
| Binary file test-data/test_bigwig_01_input_a.bw has changed |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bigwig_01_output_a.bw |
| b |
| Binary file test-data/test_bigwig_01_output_a.bw has changed |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_bigwig_01_output_a.sorted.bgr |
| b |
| Binary file test-data/test_bigwig_01_output_a.sorted.bgr has changed |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_gff_01_input_a.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gff_01_input_a.gtf Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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"; |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_gff_01_output_a__all.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gff_01_output_a__all.gtf Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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) |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_gff_01_output_a__only-matches.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gff_01_output_a__only-matches.gtf Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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"; |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_vcf_01.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf_01.fasta Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +>chr1 +CAAAAAAGCAGTTGACAGTTGTTCGGGCTTGTTACGCATCTTAAGATCGAATAAGGAGAGAGGGTCTAAACG +AGGCGCACCCCGCCTATGGGTGATCGAGGTACTAGGGGTTGGTCGCAGGTCTGTATTACCGTTAGCGGTGCA +AGGGGATCTGATCGAGTGATTCACCTACTCATGTGGCGAGCACGCCGACGAAATACTCCTGGTCGTGTTATA +AAGCCCTGGTTTTCCTTTCC +>chr2 +CACAAAATGCACGTGGATGCAGGCATTTATCCAACCCACACTATTACGTTCACCAAATGTGTGGACCAACTG +CGGGACTAGGTAAGCTTGTCCTCAATGAGCGAAATTGATATTTCTCTACCGACTTGGGGTCGACTGGACGAG +TCAGCTGTGCAACAGCTCAGCCGGTTTCGATAAACCGAAACCTTGAATGTTTGGACTTGCGTCATGGCGAAC +AAAGATCGTTCATGTCGCA \ No newline at end of file |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_vcf_01.over.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf_01.over.chain Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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 + |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_vcf_01_input.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf_01_input.vcf Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_vcf_01_output.vcf.unmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf_01_output.vcf.unmap Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_wig_01_input_a.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_wig_01_input_a.wig Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_wig_01_output_a.bw |
| b |
| Binary file test-data/test_wig_01_output_a.bw has changed |
| b |
| diff -r 000000000000 -r 5773a57e91e6 test-data/test_wig_01_output_a.sorted.bgr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_wig_01_output_a.sorted.bgr Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +chr2 89999 989999 220.0 +chr3 74999 974999 330.0 |
| b |
| diff -r 000000000000 -r 5773a57e91e6 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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. +# |
| b |
| diff -r 000000000000 -r 5773a57e91e6 tool-data/liftOver.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/liftOver.loc.sample Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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... |
| b |
| diff -r 000000000000 -r 5773a57e91e6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Sep 26 05:44:21 2017 -0400 |
| b |
| @@ -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> |