comparison pima_report.xml @ 0:0a558f444c98 draft

Uploaded
author greg
date Fri, 03 Mar 2023 22:06:23 +0000
parents
children 67d0939b56b0
comparison
equal deleted inserted replaced
-1:000000000000 0:0a558f444c98
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