Mercurial > repos > devteam > merge
annotate merge.xml @ 3:b9c97d3233bb draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:51:07 -0400 |
| parents | 1e9d95cae35f |
| children | dfbbc0291b36 |
| rev | line source |
|---|---|
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72e1fdd8e7ae
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
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changeset
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1 <tool id="gops_merge_1" name="Merge" version="1.0.0"> |
| 0 | 2 <description>the overlapping intervals of a dataset</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command> | |
| 8 <inputs> | |
| 9 <param format="interval" name="input1" type="data"> | |
| 10 <label>Merge overlaping regions of</label> | |
| 11 </param> | |
| 12 <param name="returntype" type="boolean" truevalue="-3" falsevalue=""> | |
| 13 <label>Output 3 column bed</label> | |
| 14 </param> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="input" name="output" metadata_source="input1" /> | |
| 18 </outputs> | |
| 19 <code file="operation_filter.py"> | |
| 20 <hook exec_after_process="exec_after_merge" /> | |
| 21 </code> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input1" value="1.bed" /> | |
| 25 <output name="output" file="gops-merge.dat" /> | |
| 26 <param name="returntype" value="true" /> | |
| 27 </test> | |
| 28 <test> | |
| 29 <param name="input1" value="2_mod.bed" ftype="interval"/> | |
| 30 <output name="output" file="gops_merge_diffCols.dat" /> | |
| 31 <param name="returntype" value="true" /> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="input1" value="gops_bigint.interval" /> | |
| 35 <output name="output" file="gops_merge_out2.bed" /> | |
| 36 <param name="returntype" value="true" /> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help> | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
| 43 **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. | |
| 44 | |
| 45 ----- | |
| 46 | |
| 47 **Screencasts!** | |
| 48 | |
| 49 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
| 50 | |
| 51 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
| 52 | |
| 53 ----- | |
| 54 | |
| 55 This operation merges all overlapping intervals into single intervals. | |
| 56 | |
| 57 **Example** | |
| 58 | |
| 2 | 59 .. image:: gops_merge.gif |
| 0 | 60 |
| 61 </help> | |
| 62 </tool> |