Mercurial > repos > devteam > basecoverage
annotate basecoverage.xml @ 3:0a3e3133b09d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:47:11 -0500 |
| parents | b8a9e718caa3 |
| children | 2cedec3759e4 |
| rev | line source |
|---|---|
|
1
642849141ae9
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
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> |