| Next changeset 1:b4e7244246e2 (2023-02-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42 |
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added:
hicup2juicer.xml hicup_macros.xml test-data/HiCUP_summary_report.html test-data/HiCUP_summary_report.txt test-data/chr21And22FromHg38.fasta test-data/dataset1.fastq test-data/dataset1.mapper_barchart.svg test-data/dataset1.trunc.fastq.gz test-data/dataset1.truncation_barchart.svg test-data/dataset1_2.ditag_size_distribution.svg test-data/dataset1_2.filt.bam test-data/dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg test-data/dataset1_2.filt.bam.deduplicator_uniques_barchart.svg test-data/dataset1_2.filt.sam test-data/dataset1_2.hicup.bam test-data/dataset1_2.hicup.bam.prejuicer test-data/dataset1_2.pair.bam test-data/dataset1_2.pair.bam.filter_piechart.svg test-data/dataset1_2_contiguous.filter.bam test-data/dataset1_2_invalid.filter.bam test-data/dataset1_2_re_ligation.filter.bam test-data/dataset1_2_same_circularised.filter.bam test-data/dataset1_2_same_dangling_ends.filter.bam test-data/dataset1_2_same_internal.filter.bam test-data/dataset2.fastq test-data/dataset2.mapper_barchart.svg test-data/dataset2.trunc.fastq.gz test-data/dataset2.truncation_barchart.svg test-data/digester_file.txt tool-data/bowtie2_indices.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r f8cb84c49623 hicup2juicer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicup2juicer.xml Mon Oct 24 16:09:44 2022 +0000 |
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| @@ -0,0 +1,83 @@ +<tool id="hicup2juicer" name="Hicup to juicer converter" version="@VERSION@+galaxy0"> + <description></description> + <macros> + <import>hicup_macros.xml</import> + </macros> + <expand macro="requirements_hicup" /> + <command detect_errors="exit_code"><![CDATA[ + #if $input_file.ext != 'sam': + #set ext='bam' + #else: + #set ext='sam' + #end if + ln -s '$input_file' input.$ext && + hicup2juicer input.$ext + ]]> + </command> + <inputs> + <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Output of HiCUP to convert" /> + </inputs> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${on_string}: Pairs in juicebox format" from_work_dir="*.prejuicer" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset1_2.hicup.bam"/> + <output name="output" value="dataset1_2.hicup.bam.prejuicer"/> + </test> + </tests> + <help><![CDATA[ + +HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup + +The hicup2juicer script converts HiCUP BAM/SAM files to a format compatible +with Juicer and JuiceBox( https://github.com/aidenlab/juicer ). +Outputfiles generated by this script may be converted to Juicer ".hic" files +using the "pre" command as described at: https://github.com/aidenlab/juicer/wiki/Pre + +The script does not use restriction site coordinates when generating output. + +FUNCTION + +HiCUP generates SAM/BAM files of mapped, filtered paired-end reads +constituting the sequenced valid Hi-C di-tags. These may then be analysed by a +variety of specialised tools, but before this is possible the datasets will +need parsing into an appropriate format. + +The hicup2juicer script converts HiCUP BAM/SAM files to a tab-delimited format +comprising 7 columns, with read pairs on the same line: + +<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> +str = strand (0 for forward, anything else for reverse) +chr = chromosome (must be a chromosome in the genome) +pos = position +frag = restriction site fragment +mapq = mapping quality score + +Column1: Readpair index number (starting at 1) +Column2: forward read strand (0 = positive strand, 1 = negative strand) +Column3: forward read chromosome name +Column4: forward read position +Column5: forward read fragment id (set to the dummy value 0) +Column6: reverse read strand (0 = positive strand, 1 = negative strand) +Column7: reverse read chromosome name +Column8: reverse read position +Column9: reverse read fragment id (set to the dummy value 1) +Column10: forward read MAPQ score +Column11: reverse read MAPQ score + + +COMMAND LINE OPTIONS + +--help Print help message and exit +--version Print the program version and exit +--zip Write output to a gzip file + +Full instructions on running the pipeline can be found at: +www.bioinformatics.babraham.ac.uk/projects/hicup + +Steven Wingett, Babraham Institute, Cambridge, UK +]]> + </help> + <expand macro="citation_hicup" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r f8cb84c49623 hicup_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicup_macros.xml Mon Oct 24 16:09:44 2022 +0000 |
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| @@ -0,0 +1,99 @@ +<macros> + <token name="@VERSION@">0.8.3</token> + <xml name="requirements_hicup"> + <requirements> + <requirement type="package" version="@VERSION@">hicup</requirement> + <requirement type="package" version="2.4.5">bowtie2</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> + <yield/> + </requirements> + <version_command>hicup --version</version_command> + </xml> + <xml name="citation_hicup"> + <citations> + <citation type="doi">10.12688/f1000research.7334.1</citation> + </citations> + </xml> + <xml name="reference_genome_macro"> + <conditional name="reference_genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <option value="indexed">Use a built-in genome index</option> + <option value="history">Use a genome from the history and build index</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="own_file" type="data" format="fasta" label="Select reference genome" /> + <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />--> + </when> + </conditional> + </xml> + <xml name="re1"> + <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme used e.g. A^GATCT,BglII. Some Hi-C protocols may use several enzymes. To specify several enzymes, use the ':' to separate them e.g. A^GATCT,BglII:A^AGCTT,HindIII:^GATC,DpnII. HiCUP accomodates N in restriction enzyme: e.g. :A^ANCTT"/> + </xml> + <xml name="re2"> + <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." + help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/> + </xml> + <xml name="filter_longest_shortest"> + <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/> + <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/> + </xml> + <xml name="no_fill"> + <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" + help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> + </xml> + <token name="@PAIRED-END_INPUT@"><![CDATA[ + ## Taken from cutadapt except that I don't accept space in name + #import re + #set library_type = str($library.type) + #if $library_type == 'paired': + #set input_1 = $library.input_1 + #set input_2 = $library.input_2 + #else if $library_type == 'paired_collection' + #set input_1 = $library.input_1.forward + #set input_2 = $library.input_1.reverse + #end if + + #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set ext = ".fq.gz" + #else: + #set ext = ".fq" + #end if + #set read1 = "dataset1" + $ext + ln -f -s '${input_1}' '$read1' && + + #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set ext2 = ".fq.gz" + #else: + #set ext2 = ".fq" + #end if + #set read2 = "dataset2" + $ext2 + ln -f -s '${input_2}' '$read2' && + ]]> + </token> + <xml name="input_paired"> + <conditional name="library"> + <param name="type" type="select" label="How Paired-end reads are organized"> + <option value="paired">Separately</option> + <option value="paired_collection">Paired-end Collection</option> + </param> + + <when value="paired"> + <param name="input_1" format="fastq,fastq.gz" type="data" label="FASTQ/A file #1" help="Should be of datatype "fastq.gz"or "fasta"" /> + <param name="input_2" format="fastq,fastq.gz" type="data" label="FASTQ/A file #2" help="Should be of datatype "fastq.gz"or "fasta"" /> + </when> + + <when value="paired_collection"> + <param name="input_1" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype "fastq.gz" or "fastq"" /> + </when> + + </conditional> + </xml> +</macros> |
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| diff -r 000000000000 -r f8cb84c49623 test-data/HiCUP_summary_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HiCUP_summary_report.html Mon Oct 24 16:09:44 2022 +0000 |
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| diff -r 000000000000 -r f8cb84c49623 test-data/HiCUP_summary_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HiCUP_summary_report.txt Mon Oct 24 16:09:44 2022 +0000 |
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| @@ -0,0 +1,2 @@ +File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Valid_Cis_Close Valid_Cis_Far Valid_Trans Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP +dataset1_2.hicup.bam 99742 99742 92512 92628 7230 7114 22.45 22.63 2658 2476 3885 3725 12437 12679 80762 80862 1143 1143 544 44 440 60 599 21 73 466 39 0 0 544 44 440 60 1.15 47.59 100.00 11.03 0.55 |
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| diff -r 000000000000 -r f8cb84c49623 test-data/chr21And22FromHg38.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr21And22FromHg38.fasta Mon Oct 24 16:09:44 2022 +0000 |
| b |
| b'@@ -0,0 +1,1950572 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|
| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.fastq Mon Oct 24 16:09:44 2022 +0000 |
| b |
| b'@@ -0,0 +1,398968 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+!##########################!!###########\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CTATGAAAAGAAAAGAAGAAAAGCTAGCTTGTTTACATTG\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCCCBBBBCBBCCCBBCCCCCCCCCCCCCCCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTAGCTT\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CGCATCACAAAGCTAGCTTAAGATTCCTTGTTGTTTCATC\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CACCCCCCDCCCCCCCCCCCBCCCBCCCCCCCCCCCCCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGTTTTTCCTTGCATATGTGAAGCTAGCTTTCTCATCATC\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+ATAATTCTGCAAAAGGCCATAAGCTAGCTTGCACACTGCC\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071'..b'ngth=40\n+CCCAGGCTCGTCTTAAACTCCTGGGATCAAGCGATTCTCC\n++SRR071233.15756235 NRTG514-16_0001:3:120:19400:13419 length=40\n+CCCCCCCCCCCBCCCCCCCCCCCCC@CCCCCCCCCCCCCC\n+@SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CAGAACCAAAGACAAAAACCACATGATTATCTCAATAAAT\n++SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+TGCCTCTTAGTGAGAGAATAATATATATTCTTGTATTTAT\n++SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+CCCCCCCCBCDCCCCCCCCCCCCCCCCCCCCCCCCDCCCC\n+@SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+TAATGCTTTCTACATTCAAAACACTGTGCTAAAACTAAAT\n++SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+77795:9;9<<?B<?<636:>>>><AA@AA##########\n+@SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+AGCTTCTTGCAGGATGCTTCCATAATTATGGGGAGGGGAA\n++SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBBBB=\n+@SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CCTTTAGAATTGTCCACATTGATGATAGAGAGACAAATGT\n++SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CCCCCCCBCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CATATTATTTAGAAACAGCAAGCTAGCTTCAAGACCCTGG\n++SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+AAAACAACTAAGAATGAGACCTACACTGTCAAAGGTAGCT\n++SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+CCCCCCBBCCCCCCCCCCCCCCCCCCCDCCCBBCCACCCC\n+@SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+TATAGGCTTCCATTATCTTGGCTTTTCCCCAGATGTAAAT\n++SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCBCCCC\n+@SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+GGAGCCATGGTGGCATCTGGCTGTTGGAAAGCACACAGGG\n++SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+AC=CCCCCCCCBBCCBBBBB?BBBBBBBB=BB=B>BB@BB\n+@SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+GAAGTGGAGATGAATCAGAAGACTGTTGGGGTATCGTTCT\n++SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+CCCCCCCCCCCCCCCCCCACCCCCCCCCCBC@CCCCCBCA\n+@SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+TTTGATATATGTTAGGTGCTATCTGGCATTTTAAGTATAT\n++SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+CC?CCC?=CBCCCC?B4AABB;*B2B;BB5-;>9:B<B7:\n+@SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+TTGTTCTGTACTTGGTTCATTGATAATAGGATGCCCCGTC\n++SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 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length=40\n+GGGGCAATGGAGCCCCGACCCGGCGGGCACAATCTCTGGC\n++SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+?48<?<;><>BA:?A<<>>3B###################\n+@SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CCAGAGTTCTTGCTAAAATTGGATTTTACAGGTGCATAAA\n++SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CC?CCCCCBBCCCCACCBCCACCCCCCCCBCCCCCACCCC\n' |
| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1.mapper_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.mapper_barchart.svg Mon Oct 24 16:09:44 2022 +0000 |
| b |
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| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1.trunc.fastq.gz |
| b |
| Binary file test-data/dataset1.trunc.fastq.gz has changed |
| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1.truncation_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.truncation_barchart.svg Mon Oct 24 16:09:44 2022 +0000 |
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| b'@@ -0,0 +1,1098 @@\n+@HD\tVN:1.5\tSO:queryname\n+@SQ\tSN:chr21\tLN:46709983\n+@SQ\tSN:chr22\tLN:50818468\n+@PG\tID:bowtie2\tPN:bowtie2\tVN:2.4.5\tCL:"/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome --threads 1 --reorder - --passthrough"\n+@PG\tID:HiCUP Mapper\tVN:0.8.3\n+@PG\tID:samtools\tPN:samtools\tPP:HiCUP Mapper\tVN:1.16.1\tCL:samtools view -bSh -\n+@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.15.1 (pysam)\tCL:samtools sort -n -@1 -T /tmp/tmpqwp310ym/sorted -O BAM -o /tmp/tmpqwp310ym/sorted.bam /tmp/tmprolrrufe/job_working_directory/000/1/outputs/galaxy_dataset_2f0aefeb-faca-49dc-a585-09a611400a5e.dat\n+@PG\tID:samtools.2\tPN:samtools\tPP:samtools.1\tVN:1.16.1\tCL:/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/samtools view -h ./0.bam\n+@PG\tID:HiCUP Filter\tVN:0.8.3\tDS:"Max insert 0 Min insert 0 Digest file /tmp/tmprolrrufe/files/c/8/e/dataset_c8ea51e8-38b0-4467-b22b-1b5878b2ab5f.dat"\n+@PG\tID:samtools.3\tPN:samtools\tPP:samtools.2\tVN:1.16.1\tCL:samtools view -bSh -\n+SRR071233.29547\t115\tchr22\t31119191\t42\t40M\t=\t28742824\t0\tGCCTCTAACCTACATGGCTCTGCTGCTTGAGATCCCCTCG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.29547\t179\tchr22\t28742824\t42\t40M\t=\t31119191\t0\tTGGGCGAGGCCTGAGGGAAAAGTGAGAATTGGAGGGAGAG\tCDCDBCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.80581\t99\tchr21\t27660196\t42\t40M\t=\t15297495\t0\tTGCATATTCACTAACCGGGACAGTTAAAAATTAATATATT\tCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.80581\t147\tchr21\t15297495\t0\t30M3I7M\t=\t27660196\t0\tTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGCGCGCATTCT\tCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-24\tXN:i:0\tXM:i:2\tXO:i:1\tXG:i:3\tNM:i:5\tMD:Z:31T0G4\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.88639\t99\tchr21\t16163798\t42\t40M\t=\t17128682\t0\tAAGTGTTTTTTTCCCCTCAGACTTTTCTTGTAAATCCTAT\t??>;?@@BB;;<;B@CCCCCCCCCCCCC@@CCCC@CCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.88639\t147\tchr21\t17128682\t42\t40M\t=\t16163798\t0\tCCTGCCTTACCCAGATGTACATTTTAAATTTAATCATAAA\t:<<::CACCCCCCCCACCCC@B??@BBB@BACAACCBCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.107757\t67\tchr21\t28254822\t42\t40M\tchr22\t10741070\t0\tATGCCAAAGAACAACTATATATACTATGTTCGAGGGCCAT\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:TRANS\n+SRR071233.107757\t131\tchr22\t10741070\t0\t40M\tchr21\t28254822\t0\tAGAACCTATGATACTCTGCCGGTTGTTTGAATTTTTACAA\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-20\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:0G10C5C1T20\tYT:Z:UU\tCT:Z:TRANS\n+SRR071233.140779\t67\tchr21\t46283592\t42\t40M\t=\t46219104\t0\tAATGGCAAGATGGGAGTACTCACATGATCAAAGAAATGTA\tCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCBBCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.140779\t131\tchr21\t46219104\t40\t40M\t=\t46283592\t0\tGCAAGGGAGACAAACGCAGCAGCAGCAACACAGGACGCCC\tCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-5\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:4A35\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.240793\t99\tchr21\t41242499\t42\t40M\tchr22\t11607630\t0\tAAGAATGCACTAGAAGGGGGTGCTGCCAGTCCCTTTGCTG\tCCCCCCCCCCCCCCCCCCCCDBBCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:TRANS\n+SRR071233.240793\t147\tchr22\t11607630\t0\t1M4I35M\tchr21\t41242499\t0\tAGCTAGCTTAGATGGAGATGTACTTGAAAATTAATGTTAT\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-22\tXN:i:0\tXM:i:1\tXO:i:1\tXG:i:4\tNM:i:5\tMD:Z:22G13\tYT:Z:UU\tCT:Z:TRANS\n+SRR071233.279029\t67\tchr21\t41244196\t42\t40M\t=\t41263102\t0\tCTGTTAGCACTTCTGTTCGTATTACCCATCACATCCCAAC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCD\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.279029\t131\tchr21\t41263102\t42\t40M\t=\t41244196\t0\tGATAGGTTTGTGGAATTTCCTTCTCAGTCCTAAATTTAGG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.321847\t83\tchr21\t17317716\t40\t40M\t=\t29915455\t'..b'N:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.15541829\t131\tchr22\t34910704\t3\t40M\t=\t34912503\t0\tAAAATTCTGAATAATCCTGATATTCTGCTAGAAAGCTAGC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-15\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:37T0C0T0\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.15550677\t99\tchr22\t31147885\t42\t40M\t=\t34392508\t0\tGCCAGAAACTATAGGGAAATCCAGTAGAAACAAGGGGCAG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15550677\t147\tchr22\t34392508\t42\t40M\t=\t31147885\t0\tTGAAGATCCAAATCTGTAAAACTGAGACTAAACTCTAGAA\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15563633\t83\tchr22\t27967670\t42\t40M\t=\t27147132\t0\tCACTCAGGCTCCCACACCACACACGGGTGTGGGCCACTGT\t##############C1?<3:>@B?CCBCCACBCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15563633\t163\tchr22\t27147132\t3\t40M\t=\t27967670\t0\tAAACAAGGAACCCTGAATCGAAAGGGAATCTAAAGCTAGC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:-15\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:37T0C0A0\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15590967\t67\tchr21\t23407074\t42\t40M\t=\t29297136\t0\tTGCCACTGTAATAGGTAAGCAATCATGGATAATGTGTAAA\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15590967\t131\tchr21\t29297136\t42\t40M\t=\t23407074\t0\tCACTGCTCCCGGCCGGAATCTGCATTTTAACAAGCAAACC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15603765\t115\tchr22\t26321542\t42\t40M\t=\t26328074\t0\tGCAGAGTGGCATCTGGACTTGGCACCTCCTCCCTCCCACA\tCCCCCCCCCCCCCCCCACCCCCCBCCCCCBBCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.15603765\t179\tchr22\t26328074\t42\t40M\t=\t26321542\t0\tCACAGAGGGAAGCATGCAGTGGCTTGGTCATGGCCATTGT\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.15652271\t99\tchr21\t45802811\t42\t40M\t=\t44526152\t0\tCAGGGCTAACCCTAGGGAAACCACACACAGGCCACGGAGG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15652271\t147\tchr21\t44526152\t42\t40M\t=\t45802811\t0\tTCTTCATAACCCAGATGACCAGAAAAACGCATCACAACCT\tCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15714997\t83\tchr22\t28121020\t42\t40M\t=\t28433997\t0\tGGATTAAAATTGTGAATCCATTTACTGCTTTCAGTTTTTC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15714997\t163\tchr22\t28433997\t42\t40M\t=\t28121020\t0\tAACTATTTAAAACATAGCCTAAAACCAGAAAGTATAAAGG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15717209\t99\tchr22\t27270040\t42\t40M\t=\t27754184\t0\tTCTGTGCCCAGAGGGAGAGATGCTTAAATAAATGACACTG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15717209\t147\tchr22\t27754184\t42\t40M\t=\t27270040\t0\tAGTGATGGGTAAGACAGACCCAAATGGCCAAATTTTCGAA\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15717367\t83\tchr21\t29121819\t42\t40M\t=\t29059158\t0\tAGCTGTGGTTGGGGAAAAAAGAGAGAGACCAACATTTATG\tCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15717367\t163\tchr21\t29059158\t42\t40M\t=\t29121819\t0\tATTCCAACAAAGATTAATCCAGTCCGTACTACACTATCCA\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:FAR\n+SRR071233.15726689\t67\tchr21\t26582533\t42\t25M\t=\t26575335\t0\tAAGAAAAAGGACAAGATGGAAGCTT\tCCCCCCBBBCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:25\tYT:Z:UU\tCT:Z:CLOSE\n+SRR071233.15726689\t131\tchr21\t26575335\t42\t40M\t=\t26582533\t0\tTGGAACCTAGAGAAAATCCCAGGCATACAAGCCCTTTGAG\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:40\tYT:Z:UU\tCT:Z:CLOSE\n' 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| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1_2.hicup.bam |
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| Binary file test-data/dataset1_2.hicup.bam has changed |
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| diff -r 000000000000 -r f8cb84c49623 test-data/dataset1_2.hicup.bam.prejuicer --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1_2.hicup.bam.prejuicer Mon Oct 24 16:09:44 2022 +0000 |
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| diff -r 000000000000 -r f8cb84c49623 test-data/dataset2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.fastq Mon Oct 24 16:09:44 2022 +0000 |
| b |
| b'@@ -0,0 +1,398968 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+AACCCCAGGAAAGCTAGCTTTCGTGGATTTTCTGAGGTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+GGTCAAATCTAAGCTAGCTTACTTAGAATTACAGCTCTTT\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n+@SRR071'..b'ngth=40\n+AATAAGTAAAGACAAAGCTATCTTAGCATTTTGGGAGGCT\n++SRR071233.15756235 NRTG514-16_0001:3:120:19400:13419 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCBACCCCC\n+@SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+ATTGGTTTTCAAAAGGAATGCTTCCAGCTTTTGCCCATTC\n++SRR071233.15756393 NRTG514-16_0001:3:120:19423:16561 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+GTACAGAAGCTACCTTGCTGGCTTGTACTGTGCTAGAATT\n++SRR071233.15756551 NRTG514-16_0001:3:120:19443:11373 length=40\n+CCCCBBC@CCCCCCCCCCCDCCCC@CACCB@ACCCBCC@C\n+@SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+TTTAACCACCAGGCTAGGCTGCCTCCTAAGCAGAAAGCTC\n++SRR071233.15756709 NRTG514-16_0001:3:120:19466:16073 length=40\n+@@@@@:AAA?@4>@@7:<><A6@:A52>27AAA2A:???=\n+@SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CTGTGCTTGTCCTTTCACTGTAATAAATCATAGCCATGAG\n++SRR071233.15756867 NRTG514-16_0001:3:120:19487:14719 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+GAAAATTTAGGTTCAAGGAAGGTAGCTTACCATAAATGTA\n++SRR071233.15757025 NRTG514-16_0001:3:120:19507:5307 length=40\n+CBCCCCCCCCCBCCCCCCCCCC@CCCCCCCCCCCCCCCAC\n+@SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+TTACTGAGATTCAGGGAGGGTACATTGGACATTGCTCTGG\n++SRR071233.15757183 NRTG514-16_0001:3:120:19528:12801 length=40\n+CCCCCCCCCCCCCCCCCCCB<CCCCCCCCCCCCCCCCCCC\n+@SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+TTCCTTCATGATTCTATTCAGAAAACTTTTCCCTTTTCAT\n++SRR071233.15757341 NRTG514-16_0001:3:120:19549:13328 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACBC\n+@SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+TGTGAATTCAGGTTTTACTTGGTGCATCACAACTGTCAGG\n++SRR071233.15757499 NRTG514-16_0001:3:120:19569:4795 length=40\n+CCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCCCCCC\n+@SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+GACTCTCAGCCTTCCTTTCCTTCTCTGGGGTCTGTCTGTT\n++SRR071233.15757657 NRTG514-16_0001:3:120:19591:16400 length=40\n+?BAAB=B=@@BBBB@BBB>BB@9BB@@=>B>BBBBBBBB>\n+@SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+AACCTCTTACTAGGTTATGGAACCAGCCCAGTAGTTCAGC\n++SRR071233.15757815 NRTG514-16_0001:3:120:19610:20289 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC?CCCCCBC\n+@SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+ATTGTGATCCTCTCTGATTTAGCTGTGTTTAGTTTCATAT\n++SRR071233.15757973 NRTG514-16_0001:3:120:19632:19403 length=40\n+?7/:<?<?<??<8??3<=AA9?4><???<2B@BB<B:::B\n+@SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+CTTCCCCAGAATCATTGCATGAGCTCCCACCTGCAGCCTC\n++SRR071233.15758131 NRTG514-16_0001:3:120:19651:11249 length=40\n+CCCCCCCCCCBCCBCCCCCBCBCCCCCCCBCCCCCCCCCC\n+@SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+CAAGAAAACAATAGCATATTTCAACTCACTTTGATGATCT\n++SRR071233.15758289 NRTG514-16_0001:3:120:19675:17150 length=40\n+?????<B;;@>>ACCCCCACCCBBC@CBBCCCCCCCCCBC\n+@SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+CATAAAAAGAGAACTCTGACCCACAATCTGCAGCAATTAG\n++SRR071233.15758447 NRTG514-16_0001:3:120:19696:1737 length=40\n+CCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+GATGCTGGTTCAGAACAGAAGACTCAGACCAACGCTAAGA\n++SRR071233.15758605 NRTG514-16_0001:3:120:19717:8653 length=40\n+CCACCBCACCCCCCBBBBBCCCCCCBCBCCC@CCCCC@CC\n+@SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+TGTGACGATGACACGTTTGAGAGTGCTCCCGGGACAGCAT\n++SRR071233.15758763 NRTG514-16_0001:3:120:19738:11060 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+CGGGGGACCAATANCTTGGGGGCGTCCGGCTGGGGNCAGG\n++SRR071233.15758921 NRTG514-16_0001:3:120:19762:15127 length=40\n+#############!#####################!####\n+@SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+GCAGGANNNNNNNNNTCAAAGATTCTTNANNNNNNNNNAC\n++SRR071233.15759079 NRTG514-16_0001:3:120:19785:6316 length=40\n+CCCCC#!!!!!!!!!############!#!!!!!!!!!##\n' |
| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset2.mapper_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.mapper_barchart.svg Mon Oct 24 16:09:44 2022 +0000 |
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| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset2.trunc.fastq.gz |
| b |
| Binary file test-data/dataset2.trunc.fastq.gz has changed |
| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/dataset2.truncation_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.truncation_barchart.svg Mon Oct 24 16:09:44 2022 +0000 |
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| b |
| diff -r 000000000000 -r f8cb84c49623 test-data/digester_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/digester_file.txt Mon Oct 24 16:09:44 2022 +0000 |
| [ |
| b"@@ -0,0 +1,19943 @@\n+Genome:chr21And22FromHg38\tRestriction_Enzyme1:re1_unspecified [A^AGCTT]\tRestriction_Enzyme2:None\tHicup Digester version 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|
| b |
| diff -r 000000000000 -r f8cb84c49623 tool-data/bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Mon Oct 24 16:09:44 2022 +0000 |
| b |
| @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie2 indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie2_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie2/hg18/, +#then the bowtie2_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie2/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie2_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r f8cb84c49623 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 24 16:09:44 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> +</tables> |
