Mercurial > repos > bgruening > hicup_mapper
comparison hicup_mapper.xml @ 4:99dd0efa992b draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author | bgruening |
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date | Fri, 25 May 2018 17:48:10 -0400 |
parents | 320a2d826a00 |
children | 396e8c4ebfee |
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3:f396b479c2f2 | 4:99dd0efa992b |
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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 <expand macro="stdio" /> | 7 <command detect_errors="exit_code"><![CDATA[ |
8 | |
9 <command><![CDATA[ | |
10 BOWTIE_PATH_BASH="\$(which bowtie2)" && | 8 BOWTIE_PATH_BASH="\$(which bowtie2)" && |
11 #set index_path = '' | 9 #set index_path = '' |
12 #if str($reference_genome.source) == "history": | 10 #if str($reference_genome.source) == "history": |
13 bowtie2-build "$reference_genome.own_file" genome && | 11 bowtie2-build '$reference_genome.own_file' genome && |
14 ln -s "$reference_genome.own_file" genome.fa && | 12 ln -s '$reference_genome.own_file' genome.fa && |
15 #set index_path = 'genome' | 13 #set index_path = 'genome' |
16 #else: | 14 #else: |
17 #set index_path = $reference_genome.index.fields.path | 15 #set index_path = $reference_genome.index.fields.path |
18 #end if | 16 #end if |
17 | |
18 ##Dealing with fastq and fastq.gz | |
19 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): | |
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 $input_second_sequence dataset2 && | |
32 #set input2='dataset2' | |
33 #end if | |
34 | |
35 | |
19 hicup_mapper | 36 hicup_mapper |
20 --index '$index_path' | 37 --zip |
21 --bowtie2 \$BOWTIE_PATH_BASH | 38 --threads \${GALAXY_SLOTS:-1} |
39 --index '$index_path' | |
40 --bowtie2 \$BOWTIE_PATH_BASH | |
41 $input1 | |
42 $input2 | |
22 | 43 |
23 $input_first_sequence $input_second_sequence | |
24 | |
25 ## output handling | |
26 && mv hicup_mapper_summary* hicup_mapper_summary.txt | |
27 && mv *.pair.sam result.pair.sam | |
28 && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev) | |
29 && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev) | |
30 && mv \$trunc_result_1*.mapper_barchart.svg dataset1.mapper_barchart.svg | |
31 && mv \$trunc_result_2*.mapper_barchart.svg dataset2.mapper_barchart.svg | |
32 && echo \$trunc_result_1.mapper_barchart.svg | |
33 && echo \$trunc_result_2.mapper_barchart.svg | |
34 ]]></command> | 44 ]]></command> |
35 <inputs> | 45 <inputs> |
36 <expand macro="input_files" /> | 46 <expand macro="input_files" /> |
37 <expand macro="reference_genome_macro" /> | 47 <expand macro="reference_genome_macro" /> |
38 </inputs> | 48 </inputs> |
39 <outputs> | 49 <outputs> |
40 <expand macro="mapper_output" /> | 50 <data name="hicup_mapper_summary" format="txt" 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"/> | |
52 <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> | |
53 <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> | |
41 </outputs> | 54 </outputs> |
42 <tests> | 55 <tests> |
43 <test> | 56 <test> |
44 <param name="input_first_sequence" value="dataset1.trunc.fastq" ftype="fastq"/> | 57 <param name="input_first_sequence" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/> |
45 <param name="input_second_sequence" value="dataset2.trunc.fastq" ftype="fastq"/> | 58 <param name="input_second_sequence" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/> |
46 | |
47 <conditional name="reference_genome"> | 59 <conditional name="reference_genome"> |
48 <param name="source" value="history" /> | 60 <param name="source" value="history" /> |
49 <param name="own_file" value="chr1.fa"/> | 61 <param name="own_file" value="chr21And22FromHg38.fasta"/> |
50 </conditional> | 62 </conditional> |
51 <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> | 63 <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> |
52 <output name="result_pair" file="result.pair.sam" lines_diff="8"/> | 64 <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
53 <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | 65 <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> |
54 <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | 66 <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> |
55 | |
56 </test> | 67 </test> |
57 </tests> | 68 </tests> |
58 <help><![CDATA[ | 69 <help><![CDATA[ |
59 | 70 |
60 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | 71 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ |