Mercurial > repos > iuc > circos

comparison gc_skew.xml @ 2:014a21767ac4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
parents
children df7356989ac1
comparison
equal deleted inserted replaced
1:ae9994cf526f 2:014a21767ac4
1 <?xml version="1.0"?>
2 <tool id="circos_gc_skew" name="GC Skew" version="@WRAPPER_VERSION@">
3 <description>calculates skew over genomic sequences</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s -f
11 #if $reference_genome.reference_genome_source == "history"
12 '$reference_genome.history_item'
13 #else
14 '$reference_genome.builtin.fields.path'
15 #end if
16 reference.fa &&
17
18 python '$__tool_directory__/gc_skew.py' reference.fa '$window' '$output'
19 ]]></command>
20 <inputs>
21 <conditional name="reference_genome">
22 <param label="Source for reference genome" name="reference_genome_source" type="select">
23 <option selected="True" value="history">Use a genome from history</option>
24 <option value="builtin">Use a built-in genome"</option>
25 </param>
26 <when value="history">
27 <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
28 </when>
29 <when value="builtin">
30 <param label="Select a reference genome" name="builtin" type="select">
31 <options from_data_table="all_fasta">
32 <filter column="2" type="sort_by" />
33 <validator message="No genomes are available for the selected input dataset" type="no_options" />
34 </options>
35 </param>
36 </when>
37 </conditional>
38 <param argument="window" type="integer" min="1" value="100000" label="Window size" />
39 </inputs>
40 <outputs>
41 <data name="output" format="bigwig" />
42 </outputs>
43 <tests>
44 <test>
45 <conditional name="reference_genome">
46 <param name="reference_genome_source" value="history" />
47 <param name="history_item" value="gc_skew/1.fa" ftype="fasta"/>
48 </conditional>
49 <param name="window" value="2" />
50 <output name="output" file="gc_skew/1.bw" ftype="bigwig" />
51 </test>
52 </tests>
53 <help><![CDATA[
54 Calculate GC skew (G-C)/(G+C) for multiple windows along the sequence.
55
56 Returns a list of ratios (floats), controlled by the length of the sequence and the size of the window.
57
58 Returns 0 for windows without any G/C by handling zero division errors.
59
60 Does NOT look at any ambiguous nucleotides.
61 ]]></help>
62 <expand macro="citations" />
63 </tool>