comparison glimmer_acgt_content.xml @ 0:4c74f770979d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:08:46 -0500
parents
children 4e87d6ebea62
comparison
equal deleted inserted replaced
-1:000000000000 0:4c74f770979d
1 <tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@">
2 <description>of windows in each sequence</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command><![CDATA[
8 window-acgt
9 $percentage
10 $input_win_len
11 $input_win_skip
12 < '$infile' > '$output'
13
14 ##TODO prettify the output
15 ]]></command>
16 <inputs>
17 <param name="infile" type="data" format="fasta" label="Genome Sequence"/>
18 <param name="input_win_len" type="integer" value="10" label="The width of the sliding window"/>
19 <param name="input_win_skip" type="integer" value="10" label="The number of positions between windows to report"/>
20 <param name="percentage" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Report percentages instead of counts"/>
21 </inputs>
22 <outputs>
23 <data name="output" format="tabular"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="infile" value="streptomyces_Tu6071_genomic.fasta" />
28 <output name="output" file="streptomyces_Tu6071_genomic.acgt" />
29 </test>
30 </tests>
31 <help>
32 <![CDATA[
33
34 **What it does**
35
36 This tool calculates the ACGT-Content from a given Sequence, given a sliding window.
37
38 -------
39
40 **Output**
41
42 Output is in the format:
43
44 window-start window-len A's C's G's T's #other %GC
45
46 Note the last window in the sequence can be shorter than *window-len* if the sequence ends prematurely
47 ]]>
48 </help>
49 <expand macro="citation" />
50 </tool>