Mercurial > repos > greg > pima_report
comparison pima_report.xml @ 0:0a558f444c98 draft
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author | greg |
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date | Fri, 03 Mar 2023 22:06:23 +0000 |
parents | |
children | 67d0939b56b0 |
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-1:000000000000 | 0:0a558f444c98 |
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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 |