|
0
|
1 <tool id="fasta_extract" name="Extract fasta sequences" version="1.0.0">
|
|
|
2 <description>using coordinates from assembled genomes</description>
|
|
|
3 <macros>
|
|
|
4 <import>fasta_extract_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
|
7 <command>
|
|
|
8 <![CDATA[
|
|
|
9 mkdir -p output_dir &&
|
|
6
|
10 mkdir -p output_orphan_dir &&
|
|
0
|
11 python $__tool_directory__/fasta_extract.py
|
|
|
12 #for $i in $inputs:
|
|
8
|
13 --input "$i" ${i.hid}
|
|
0
|
14 #end for
|
|
|
15 #if str($reference_genome_cond.reference_genome_source) == "cached":
|
|
9
|
16 #set genome_file = $reference_genome_cond.reference_genome.fields.path
|
|
0
|
17 #else:
|
|
9
|
18 #set genome_file = $reference_genome_cond.reference_genome
|
|
0
|
19 #end if
|
|
9
|
20 --genome_file "$genome_file"
|
|
0
|
21 --subtract_from_start $subtract_from_start
|
|
|
22 --add_to_end $add_to_end
|
|
|
23 --extend_existing $extend_existing
|
|
|
24 --strand $strand
|
|
|
25 ]]>
|
|
|
26 </command>
|
|
|
27 <inputs>
|
|
|
28 <param name="inputs" type="data" format="gff" multiple="True" label="Fetch sequences for intervals in">
|
|
|
29 <validator type="unspecified_build" />
|
|
|
30 </param>
|
|
|
31 <conditional name="reference_genome_cond">
|
|
|
32 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
|
|
|
33 <option value="cached">Locally Cached</option>
|
|
|
34 <option value="history">From History</option>
|
|
|
35 </param>
|
|
|
36 <when value="cached">
|
|
|
37 <param name="reference_genome" type="select" label="Using reference genome">
|
|
|
38 <options from_data_table="all_fasta" />
|
|
|
39 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
|
|
|
40 </param>
|
|
|
41 </when>
|
|
|
42 <when value="history">
|
|
|
43 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
|
|
|
44 </when>
|
|
|
45 </conditional>
|
|
|
46 <param name="subtract_from_start" type="integer" value="50" min="0" label="Distance to subtract from start" />
|
|
|
47 <param name="add_to_end" type="integer" value="50" min="0" label="Distance to add to end" />
|
|
|
48 <param name="extend_existing" type="select" label="Extend existing start and end coordinates or extend from computed midpoint?">
|
|
|
49 <option value="midpoint" selected="True">Extend from computed midpoint</option>
|
|
|
50 <option value="existing">Extend from existing start and end coordinates</option>
|
|
|
51 </param>
|
|
|
52 <param name="strand" type="select" label="Extract reverse complement sequence on reverse strand?">
|
|
|
53 <option value="no" selected="True">No</option>
|
|
|
54 <option value="yes">Yes</option>
|
|
|
55 </param>
|
|
|
56 </inputs>
|
|
|
57 <outputs>
|
|
6
|
58 <collection name="fasta_extract_output_orphan" type="list" label="Extract fasta sequences (orphans) on ${on_string}">
|
|
|
59 <discover_datasets pattern="(?P<designation>.*)" directory="output_orphan_dir" ext="gff" visible="false" />
|
|
|
60 </collection>
|
|
|
61 <collection name="fasta_extract_output" type="list" label="Extract fasta sequences on ${on_string}">
|
|
0
|
62 <discover_datasets pattern="(?P<designation>.*)" directory="output_dir" ext="fasta" visible="false" />
|
|
|
63 </collection>
|
|
|
64 </outputs>
|
|
|
65 <tests>
|
|
|
66 <test>
|
|
|
67 </test>
|
|
|
68 </tests>
|
|
|
69 <help>
|
|
|
70
|
|
|
71 **What it does**
|
|
|
72
|
|
|
73 </help>
|
|
|
74 <expand macro="citations" />
|
|
|
75 </tool>
|
