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comparison draw_features.xml @ 0:636eeb4fb9ac draft

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author greg
date Wed, 25 Jan 2023 20:38:21 +0000
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1 <tool id="draw_features" name="PIMA: draw features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>of annotated assemblies</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 #if $contigs.is_of_type('fasta.gz'):
11 gunzip -c '$contigs' > 'contigs.fasta' &&
12 #else:
13 ln -s '$contigs' 'contigs.fasta' &&
14 #end if
15
16 mkdir feature_hits_dir &&
17 mkdir output_dir &&
18
19 #for $i in $feature_hits:
20 #set file_name = $i.file_name
21 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
22 ln -s '$file_name' 'feature_hits_dir/$identifier' &&
23 #end for
24
25 python '$__tool_directory__/draw_features.py'
26 --contigs 'contigs.fasta'
27 --feature_hits_dir 'feature_hits_dir'
28 --output_dir 'output_dir'
29 #if str($output_process_log) == 'yes':
30 && mv 'process_log' '$process_log'
31 #end if
32 ]]></command>
33 <inputs>
34 <param name="contigs" type="data" format="fasta,fasta.gz" label="Fasta file of assembled contigs"/>
35 <param name="feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/>
36 <param name="output_process_log" type="select" display="radio" label="Output process log file?">
37 <option value="no" selected="true">No</option>
38 <option value="yes">Yes</option>
39 </param>
40 </inputs>
41 <outputs>
42 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (Process log)">
43 <filter>output_process_log == 'yes'</filter>
44 </data>
45 <collection name="features_png" type="list" format="png">
46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_dir"/>
47 </collection>
48 </outputs>
49 <tests>
50 <test>
51 <param name="contigs" value="PS01519_contigs.fasta.gz" ftype="fasta.gz"/>
52 <param name="feature_hits">
53 <collection type="list">
54 <element name="amr_cds.bed" value="amr_cds.bed"/>
55 </collection>
56 </param>
57 <output_collection name="features_png" type="list" count="1">
58 <element name="contig_1" ftype="png">
59 <assert_contents>
60 <has_size value="25383" delta="100"/>
61 </assert_contents>
62 </element>
63 </output_collection>
64 </test>
65 </tests>
66 <help>
67 **What it does**
68
69 Accepts a FASTA file of assembled contigs and a collection of 2 BED files containing the feature hits and plots
70 the features.
71 </help>
72 <expand macro="citations"/>
73 </tool>
74