| Previous changeset 4:99dd0efa992b (2018-05-25) Next changeset 6:70427be35bf2 (2022-10-24) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef |
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modified:
hicup_macros.xml hicup_mapper.xml test-data/HiCUP_summary_report.html test-data/HiCUP_summary_report.txt 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.hicup.bam 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.mapper_barchart.svg test-data/dataset2.trunc.fastq.gz test-data/dataset2.truncation_barchart.svg test-data/digester_file.txt |
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added:
test-data/dataset1_2.filt.sam |
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removed:
test-data/hicup_deduplicator_summary.txt test-data/hicup_filter_summary.txt test-data/hicup_mapper_summary.txt test-data/hicup_truncater_summary.txt |
| b |
| diff -r 99dd0efa992b -r 396e8c4ebfee hicup_macros.xml --- a/hicup_macros.xml Fri May 25 17:48:10 2018 -0400 +++ b/hicup_macros.xml Sat Oct 22 08:43:54 2022 +0000 |
| [ |
| @@ -1,11 +1,10 @@ <macros> - <token name="@VERSION@">0.6.1</token> + <token name="@VERSION@">0.8.3</token> <xml name="requirements_hicup"> <requirements> <requirement type="package" version="@VERSION@">hicup</requirement> - <requirement type="package" version="2.2.6">bowtie2</requirement> - <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="0.13.1">docutils</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> @@ -35,12 +34,8 @@ </when> </conditional> </xml> - <xml name="input_files"> - <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/> - <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/> - </xml> <xml name="re1"> - <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> + <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." @@ -54,4 +49,51 @@ <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> |
| b |
| diff -r 99dd0efa992b -r 396e8c4ebfee hicup_mapper.xml --- a/hicup_mapper.xml Fri May 25 17:48:10 2018 -0400 +++ b/hicup_mapper.xml Sat Oct 22 08:43:54 2022 +0000 |
| [ |
| @@ -1,9 +1,9 @@ -<tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@.0"> +<tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@+galaxy0"> <description>aligns paired reads independently to a reference genome and retains reads where both partners align.</description> <macros> <import>hicup_macros.xml</import> </macros> - <expand macro="requirements_hicup" /> + <expand macro="requirements_hicup"/> <command detect_errors="exit_code"><![CDATA[ BOWTIE_PATH_BASH="\$(which bowtie2)" && #set index_path = '' @@ -15,62 +15,84 @@ #set index_path = $reference_genome.index.fields.path #end if - ##Dealing with fastq and fastq.gz - #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): - ln -s $input_first_sequence dataset1.gz && - #set input1='dataset1.gz' - #else - ln -s $input_first_sequence dataset1 && - #set input1='dataset1' - #end if - - #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): - ln -s $input_second_sequence dataset2.gz && - #set input2='dataset2.gz' - #else - ln -s $input_second_sequence dataset2 && - #set input2='dataset2' - #end if - + ##Dealing with inputs + @PAIRED-END_INPUT@ hicup_mapper --zip --threads \${GALAXY_SLOTS:-1} --index '$index_path' --bowtie2 \$BOWTIE_PATH_BASH - $input1 - $input2 + '$read1' + '$read2' ]]></command> <inputs> - <expand macro="input_files" /> - <expand macro="reference_genome_macro" /> + <expand macro="input_paired"/> + <expand macro="reference_genome_macro"/> </inputs> <outputs> - <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> + <data name="hicup_mapper_summary" format="tabular" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> - <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> - <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> + <collection type="list" name="mapper_barchart" label="Mapper Barchart.svg"> + <discover_datasets pattern="(?P<designation>.+)\.mapper_barchart\.svg$" directory="./" ext="svg"/> + </collection> </outputs> - <tests> + <tests> <test> - <param name="input_first_sequence" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/> - <param name="input_second_sequence" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/> + <conditional name="library"> + <param name="type" value="paired"/> + <param name="input_1" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/> + <param name="input_2" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/> + </conditional> <conditional name="reference_genome"> - <param name="source" value="history" /> + <param name="source" value="history"/> <param name="own_file" value="chr21And22FromHg38.fasta"/> </conditional> - <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> - <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> - <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> + <output name="hicup_mapper_summary"> + <assert_contents> + <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/> + <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/> + </assert_contents> + </output> + <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/> + <output_collection name="mapper_barchart" count="2"> + <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/> + <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/> + </output_collection> + </test> + <test> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" ftype="fastq.gz" value="dataset1.trunc.fastq.gz"/> + <element name="reverse" ftype="fastq.gz" value="dataset2.trunc.fastq.gz"/> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history"/> + <param name="own_file" value="chr21And22FromHg38.fasta"/> + </conditional> + <output name="hicup_mapper_summary"> + <assert_contents> + <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/> + <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/> + </assert_contents> + </output> + <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/> + <output_collection name="mapper_barchart" count="2"> + <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/> + <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/> + </output_collection> </test> </tests> <help><![CDATA[ - For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ + For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html - To get more information about the mapper visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Mapper + To get more information about the mapper visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-mapper ]]></help> - <expand macro="citation_hicup" /> + <expand macro="citation_hicup"/> </tool> |
| b |
| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/HiCUP_summary_report.html --- a/test-data/HiCUP_summary_report.html Fri May 25 17:48:10 2018 -0400 +++ b/test-data/HiCUP_summary_report.html Sat Oct 22 08:43:54 2022 +0000 |
| [ |
| b'@@ -1,661 +1,3694 @@\n-\xef\xbb\xbf<!DOCTYPE html>\n+<!DOCTYPE html>\n+\n <html>\n+\n <head>\n-\t<meta http-equiv="content-type" content="text/html; charset=UTF-8">\n-\t<title>HiCUP Processing Report - dataset1_2</title>\n-\t<style type="text/css">\n-\t\tbody {\n-\t\t\tfont-family: Arial, sans-serif;\n-\t\t\tfont-size:14px;\n-\t\t\tpadding:0 20px 20px;\n-\t\t}\n-\t\t.container {\n-\t\t\tmargin:0 auto;\n-\t\t\tmax-width:1200px;\n-\t\t}\n-\t\t.header_title {\n-\t\t\tfloat:left;\n-\t\t}\n-\t\t.header_subtitle {\n-\t\t\tfloat:right;\n-\t\t\ttext-align:right;\n-\t\t\tmargin-top:40px;\n-\t\t}\n-\t\t.header_subtitle h4,\n-\t\t.header_subtitle p {\n-\t\t\tmargin:0;\n-\t\t}\n-\t\th1 {\n-\t\t\tfont-size: 3.2em;\n-\t\t}\n-\t\th2 {\n-\t\t\tfont-size:2.2em;\n-\t\t}\n-\t\th3 {\n-\t\t\tfont-size:1.8em;\n-\t\t}\n-\t\th4 {\n-\t\t\tfont-size:1.4em;\n-\t\t}\n-\t\th3, h4, hr {\n-\t\t\tclear:both;\n-\t\t}\n-\t\thr {\n-\t\t\tborder-top:1px solid #CCC;\n-\t\t\tborder-bottom:1px solid #F3F3F3;\n-\t\t\tborder-left:0;\n-\t\t\tborder-right:0;\n-\t\t\theight:0;\n-\t\t}\n-\t\ta img {\n-\t\t\tborder:0;\n-\t\t}\n-\t\t.data {\n-\t\t\tfloat:left;\n-\t\t\twidth:500px;\n-\t\t\tmax-width:100%;\n-\t\t\tmargin-right:30px;\n-\t\t}\n-\t\t.data_table {\n-\t\t\tborder:1px solid #CCC;\n-\t\t\tborder-collapse:separate;\n-\t\t\tborder-spacing: 0;\n-\t\t\tborder-left:0;\n-\t\t\t-webkit-border-radius:4px;\n-\t\t\t-moz-border-radius:4px;\n-\t\t\tborder-radius:4px;\n-\t\t\tmargin-bottom:30px;\n-\t\t}\n-\t\t.data_table th, .data_table td {\n-\t\t\tborder-left:1px solid #CCC;\n-\t\t\tborder-top:1px solid #CCC;\n-\t\t\tpadding:5px 7px;\n-\t\t}\n-\t\t.data_table thead tr th,\n-\t\t.data_table thead tr td {\n-\t\t\ttext-align:right;\n-\t\t\tborder-top:0;\n-\t\t\tborder-bottom: 2px solid #666;\n-\t\t}\n-\t\t.data_table tbody tr:first-child th,\n-\t\t.data_table tbody tr:first-child td {\n-\t\t\tborder-top:0;\n-\t\t}\n-\t\t\n-\t\t.data_table th {\n-\t\t\ttext-align:left;\n-\t\t}\n-\t\t.data_table td {\n-\t\t\ttext-align:right;\n-\t\t}\n-\t\t.data_table tfoot th,\n-\t\t.data_table tfoot td {\n-\t\t\tborder-top: 2px solid #666;\n-\t\t}\n-\t\t\n-\t\t.plot {\n-\t\t\twidth:650px;\n-\t\t\tmax-width:100%;\n-\t\t\tfloat:left;\n-\t\t\tmargin-bottom:30px;\n-\t\t}\n-\t\t#ditag_length_plot {\n-\t\t\twidth:100%;\n-\t\t\theight:600px;\n-\t\t}\n-\t\t\n-\t\tfooter {\n-\t\t\tcolor:#999;\n-\t\t}\n-\t\tfooter a {\n-\t\t\tcolor:#999;\n-\t\t}\n-\t</style>\n+\n+<meta charset="utf-8" />\n+<meta name="generator" content="pandoc" />\n+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />\n+\n+\n+\n+\n+<title>HiCUP Summary Report</title>\n+\n+<script>// Pandoc 2.9 adds attributes on both header and div. 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| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/dataset1_2.filt.bam |
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| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/dataset2.trunc.fastq.gz |
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| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/digester_file.txt --- a/test-data/digester_file.txt Fri May 25 17:48:10 2018 -0400 +++ b/test-data/digester_file.txt Sat Oct 22 08:43:54 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -Genome:chr21And22FromHg38 Restriction_Enzyme1:re1_unspecified [A^AGCTT] Restriction_Enzyme2:None Hicup digester version 0.6.1 +Genome:chr21And22FromHg38 Restriction_Enzyme1:re1_unspecified [A^AGCTT] Restriction_Enzyme2:None Hicup Digester version 0.8.3 Chromosome Fragment_Start_Position Fragment_End_Position Fragment_Number RE1_Fragment_Number 5'_Restriction_Site 3'_Restriction_Site chr21 1 5011282 1 1 None Re1 chr21 5011283 5011467 2 2 Re1 Re1 |
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| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/hicup_deduplicator_summary.txt --- a/test-data/hicup_deduplicator_summary.txt Fri May 25 17:48:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques -dataset1_2.filt.bam 543 543 43 440 60 |
| b |
| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/hicup_filter_summary.txt --- a/test-data/hicup_filter_summary.txt Fri May 25 17:48:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size -dataset1_2.pair.bam 1143 543 43 440 60 600 22 75 474 29 0 0 |
| b |
| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/hicup_mapper_summary.txt --- a/test-data/hicup_mapper_summary.txt Fri May 25 17:48:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired -dataset1.trunc.fastq.gz 99742 2658 2.7 3885 3.9 12437 12.5 80762 81.0 1143 1.1 -dataset2.trunc.fastq.gz 99742 2476 2.5 3725 3.7 12679 12.7 80862 81.1 1143 1.1 |
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| diff -r 99dd0efa992b -r 396e8c4ebfee test-data/hicup_truncater_summary.txt --- a/test-data/hicup_truncater_summary.txt Fri May 25 17:48:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence -dataset1.fastq 99742 7230 7.25 92512 92.75 22.45 -dataset2.fastq 99742 7114 7.13 92628 92.87 22.63 |
