Mercurial > repos > bgruening > hicup_mapper
comparison hicup_mapper.xml @ 5:396e8c4ebfee draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author | bgruening |
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date | Sat, 22 Oct 2022 08:43:54 +0000 |
parents | 99dd0efa992b |
children | be104dee2833 |
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4:99dd0efa992b | 5:396e8c4ebfee |
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1 <tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@.0"> | 1 <tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@+galaxy0"> |
2 <description>aligns paired reads independently to a reference genome and retains reads where both partners align.</description> | 2 <description>aligns paired reads independently to a reference genome and retains reads where both partners align.</description> |
3 <macros> | 3 <macros> |
4 <import>hicup_macros.xml</import> | 4 <import>hicup_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements_hicup" /> | 6 <expand macro="requirements_hicup"/> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 BOWTIE_PATH_BASH="\$(which bowtie2)" && | 8 BOWTIE_PATH_BASH="\$(which bowtie2)" && |
9 #set index_path = '' | 9 #set index_path = '' |
10 #if str($reference_genome.source) == "history": | 10 #if str($reference_genome.source) == "history": |
11 bowtie2-build '$reference_genome.own_file' genome && | 11 bowtie2-build '$reference_genome.own_file' genome && |
13 #set index_path = 'genome' | 13 #set index_path = 'genome' |
14 #else: | 14 #else: |
15 #set index_path = $reference_genome.index.fields.path | 15 #set index_path = $reference_genome.index.fields.path |
16 #end if | 16 #end if |
17 | 17 |
18 ##Dealing with fastq and fastq.gz | 18 ##Dealing with inputs |
19 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): | 19 @PAIRED-END_INPUT@ |
20 ln -s $input_first_sequence dataset1.gz && | |
21 #set input1='dataset1.gz' | |
22 #else | |
23 ln -s $input_first_sequence dataset1 && | |
24 #set input1='dataset1' | |
25 #end if | |
26 | |
27 #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): | |
28 ln -s $input_second_sequence dataset2.gz && | |
29 #set input2='dataset2.gz' | |
30 #else | |
31 ln -s $input_second_sequence dataset2 && | |
32 #set input2='dataset2' | |
33 #end if | |
34 | |
35 | 20 |
36 hicup_mapper | 21 hicup_mapper |
37 --zip | 22 --zip |
38 --threads \${GALAXY_SLOTS:-1} | 23 --threads \${GALAXY_SLOTS:-1} |
39 --index '$index_path' | 24 --index '$index_path' |
40 --bowtie2 \$BOWTIE_PATH_BASH | 25 --bowtie2 \$BOWTIE_PATH_BASH |
41 $input1 | 26 '$read1' |
42 $input2 | 27 '$read2' |
43 | 28 |
44 ]]></command> | 29 ]]></command> |
45 <inputs> | 30 <inputs> |
46 <expand macro="input_files" /> | 31 <expand macro="input_paired"/> |
47 <expand macro="reference_genome_macro" /> | 32 <expand macro="reference_genome_macro"/> |
48 </inputs> | 33 </inputs> |
49 <outputs> | 34 <outputs> |
50 <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> | 35 <data name="hicup_mapper_summary" format="tabular" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> |
51 <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> | 36 <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> |
52 <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> | 37 <collection type="list" name="mapper_barchart" label="Mapper Barchart.svg"> |
53 <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> | 38 <discover_datasets pattern="(?P<designation>.+)\.mapper_barchart\.svg$" directory="./" ext="svg"/> |
39 </collection> | |
54 </outputs> | 40 </outputs> |
55 <tests> | 41 <tests> |
56 <test> | 42 <test> |
57 <param name="input_first_sequence" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/> | 43 <conditional name="library"> |
58 <param name="input_second_sequence" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/> | 44 <param name="type" value="paired"/> |
45 <param name="input_1" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/> | |
46 <param name="input_2" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/> | |
47 </conditional> | |
59 <conditional name="reference_genome"> | 48 <conditional name="reference_genome"> |
60 <param name="source" value="history" /> | 49 <param name="source" value="history"/> |
61 <param name="own_file" value="chr21And22FromHg38.fasta"/> | 50 <param name="own_file" value="chr21And22FromHg38.fasta"/> |
62 </conditional> | 51 </conditional> |
63 <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> | 52 <output name="hicup_mapper_summary"> |
64 <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 53 <assert_contents> |
65 <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | 54 <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"/> |
66 <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | 55 <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"/> |
56 </assert_contents> | |
57 </output> | |
58 <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/> | |
59 <output_collection name="mapper_barchart" count="2"> | |
60 <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/> | |
61 <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/> | |
62 </output_collection> | |
63 </test> | |
64 <test> | |
65 <conditional name="library"> | |
66 <param name="type" value="paired_collection"/> | |
67 <param name="input_1"> | |
68 <collection type="paired"> | |
69 <element name="forward" ftype="fastq.gz" value="dataset1.trunc.fastq.gz"/> | |
70 <element name="reverse" ftype="fastq.gz" value="dataset2.trunc.fastq.gz"/> | |
71 </collection> | |
72 </param> | |
73 </conditional> | |
74 <conditional name="reference_genome"> | |
75 <param name="source" value="history"/> | |
76 <param name="own_file" value="chr21And22FromHg38.fasta"/> | |
77 </conditional> | |
78 <output name="hicup_mapper_summary"> | |
79 <assert_contents> | |
80 <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"/> | |
81 <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"/> | |
82 </assert_contents> | |
83 </output> | |
84 <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/> | |
85 <output_collection name="mapper_barchart" count="2"> | |
86 <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/> | |
87 <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/> | |
88 </output_collection> | |
67 </test> | 89 </test> |
68 </tests> | 90 </tests> |
69 <help><![CDATA[ | 91 <help><![CDATA[ |
70 | 92 |
71 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | 93 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html |
72 | 94 |
73 To get more information about the mapper visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Mapper | 95 To get more information about the mapper visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-mapper |
74 ]]></help> | 96 ]]></help> |
75 <expand macro="citation_hicup" /> | 97 <expand macro="citation_hicup"/> |
76 </tool> | 98 </tool> |