|
0
|
1 <tool id="pima_report" name="PIMA: summary report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
|
|
|
2 <description></description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements"/>
|
|
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
|
8 #import re
|
|
|
9
|
|
|
10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
|
|
|
11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
|
|
|
12
|
|
|
13 mkdir feature_bed_dir &&
|
|
|
14 mkdir feature_png_dir &&
|
|
|
15 mkdir mutation_regions_dir &&
|
|
|
16 touch 'pima_report.pdf' &&
|
|
|
17
|
|
|
18 #for $i in $features_bed:
|
|
|
19 #set file_name = $i.file_name
|
|
|
20 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
|
|
|
21 ln -s $i 'feature_bed_dir/$identifier' &&
|
|
|
22 #end for
|
|
|
23 #for $i in $features_png:
|
|
|
24 #set file_name = $i.file_name
|
|
|
25 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
|
|
|
26 ln -s $i 'feature_png_dir/$identifier' &&
|
|
|
27 #end for
|
|
|
28 #for $i in $mutation_regions:
|
|
|
29 #set file_name = $i.file_name
|
|
|
30 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
|
|
|
31 ln -s $i 'mutation_regions_dir/$identifier' &&
|
|
|
32 #end for
|
|
|
33
|
|
|
34 python '${__tool_directory__}/pima_report.py'
|
|
|
35 --analysis_name '$analysis_name'
|
|
|
36 --assembly_fasta_file '$assembly_fasta_file'
|
|
|
37 --assembly_name '$assembly_name'
|
|
|
38 --contig_coverage_file '$contig_coverage_file'
|
|
|
39 --dbkey '$aligned_sample.metadata.dbkey'
|
|
|
40 --feature_bed_dir 'feature_bed_dir'
|
|
|
41 --feature_png_dir 'feature_png_dir'
|
|
|
42 #if $illumina_fastq_file.ext.endswith(".gz"):
|
|
|
43 --gzipped
|
|
|
44 #end if
|
|
|
45 --illumina_fastq_file '$illumina_fastq_file'
|
|
|
46 --mutation_regions_dir 'mutation_regions_dir'
|
|
|
47 --mutation_regions_bed_file '$mutation_regions_bed_file'
|
|
|
48 --pima_css '${__tool_directory__}/pima.css'
|
|
|
49 && mv 'pima_report.pdf' '$output'
|
|
|
50 ]]></command>
|
|
|
51 <inputs>
|
|
|
52 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
|
|
|
53 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
|
|
|
54 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
|
|
|
55 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
|
|
|
56 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
|
|
|
57 <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
|
|
|
58 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
|
|
|
59 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
|
|
|
60 </inputs>
|
|
|
61 <outputs>
|
|
|
62 <data name="output" format="pdf"/>
|
|
|
63 </outputs>
|
|
|
64 <tests>
|
|
|
65 <test>
|
|
|
66 <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
|
|
|
67 <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
|
|
|
68 <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
|
|
|
69 <param name="illumina_fastq_file" value="illumina_fastq.fastq" ftype="fastq"/>
|
|
|
70 <output name="output" value="output.pdf" ftype="pdf"/>
|
|
|
71 </test>
|
|
|
72 </tests>
|
|
|
73 <help>
|
|
|
74 **What it does**
|
|
|
75
|
|
|
76 Generates the PIMA analysis summary report.
|
|
|
77 </help>
|
|
|
78 <expand macro="citations"/>
|
|
|
79 </tool>
|
|
|
80
|
