Mercurial > repos > bgruening > glimmer_acgt_content
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 |
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date | Tue, 28 Nov 2017 10:08:46 -0500 |
parents | |
children | 4e87d6ebea62 |
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-1:000000000000 | 0:4c74f770979d |
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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> |