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comparison fasta_extract.xml @ 0:bc3f2a5c7b53 draft

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author greg
date Sun, 10 Jan 2016 13:03:12 -0500
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-1:000000000000 0:bc3f2a5c7b53
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 &&
10 python $__tool_directory__/fasta_extract.py
11 #for $i in $inputs:
12 --input "$i" "${i.hid}"
13 #end for
14 #if str($reference_genome_cond.reference_genome_source) == "cached":
15 #set genome_file = $reference_genome_cond.reference_genome.fields.path
16 #else:
17 #set genome_file = $reference_genome_cond.reference_genome
18 #end if
19 --genome_file "$genome_file"
20 --subtract_from_start $subtract_from_start
21 --add_to_end $add_to_end
22 --extend_existing $extend_existing
23 --strand $strand
24 ]]>
25 </command>
26 <inputs>
27 <param name="inputs" type="data" format="gff" multiple="True" label="Fetch sequences for intervals in">
28 <validator type="unspecified_build" />
29 </param>
30 <conditional name="reference_genome_cond">
31 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
32 <option value="cached">Locally Cached</option>
33 <option value="history">From History</option>
34 </param>
35 <when value="cached">
36 <param name="reference_genome" type="select" label="Using reference genome">
37 <options from_data_table="all_fasta" />
38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
39 </param>
40 </when>
41 <when value="history">
42 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
43 </when>
44 </conditional>
45 <param name="subtract_from_start" type="integer" value="50" min="0" label="Distance to subtract from start" />
46 <param name="add_to_end" type="integer" value="50" min="0" label="Distance to add to end" />
47 <param name="extend_existing" type="select" label="Extend existing start and end coordinates or extend from computed midpoint?">
48 <option value="midpoint" selected="True">Extend from computed midpoint</option>
49 <option value="existing">Extend from existing start and end coordinates</option>
50 </param>
51 <param name="strand" type="select" label="Extract reverse complement sequence on reverse strand?">
52 <option value="no" selected="True">No</option>
53 <option value="yes">Yes</option>
54 </param>
55 </inputs>
56 <outputs>
57 <collection name="fasta_extract_output" type="list" label="Extract fasta sequences ${on_string}">
58 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_dir" ext="fasta" visible="false" />
59 </collection>
60 </outputs>
61 <tests>
62 <test>
63 </test>
64 </tests>
65 <help>
66
67 **What it does**
68
69 </help>
70 <expand macro="citations" />
71 </tool>