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annotate basecoverage.xml @ 4:346e0034714a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author | devteam |
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date | Fri, 18 Dec 2015 19:36:36 -0500 |
parents | 057d57cf718d |
children | 37652c34b3bf |
rev | line source |
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1
d00c8ea7792c
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
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1 <tool id="gops_basecoverage_1" name="Base Coverage" version="1.0.0"> |
0 | 2 <description>of all intervals</description> |
3 <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command> | |
4 <requirements> | |
5 <requirement type="package" version="0.7.1">bx-python</requirement> | |
6 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
7 </requirements> | |
8 <inputs> | |
9 <param format="interval" name="input1" type="data"> | |
10 <label>Compute coverage for</label> | |
11 </param> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="txt" name="output" /> | |
15 </outputs> | |
16 <code file="operation_filter.py"/> | |
17 <tests> | |
18 <test> | |
19 <param name="input1" value="1.bed" /> | |
20 <output name="output" file="gops_basecoverage_out.txt" /> | |
21 </test> | |
22 <test> | |
23 <param name="input1" value="gops_bigint.interval" /> | |
24 <output name="output" file="gops_basecoverage_out2.txt" /> | |
25 </test> | |
26 </tests> | |
27 <help> | |
28 | |
29 .. class:: infomark | |
30 | |
31 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. | |
32 | |
33 This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total. | |
34 | |
35 ----- | |
36 | |
37 **Screencasts!** | |
38 | |
39 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
40 | |
41 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
42 | |
43 **Example** | |
44 | |
2 | 45 .. image:: gops_baseCoverage.gif |
0 | 46 |
47 | |
48 </help> | |
49 </tool> |