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annotate complement.xml @ 4:1b2bfb9981b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 19:37:08 -0500 |
| parents | a3c7fd2ae338 |
| children | 1377a23bc02a |
| rev | line source |
|---|---|
|
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8f2c476e92ed
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
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changeset
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1 <tool id="gops_complement_1" name="Complement" version="1.0.0"> |
| 0 | 2 <description>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_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command> | |
| 8 <inputs> | |
| 9 <param format="interval" name="input1" type="data"> | |
| 10 <label>Complement regions of</label> | |
| 11 </param> | |
| 12 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement"> | |
| 13 </param> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="input" name="output" metadata_source="input1" /> | |
| 17 </outputs> | |
| 18 <code file="operation_filter.py"/> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="input1" value="1.bed" dbkey="hg17" /> | |
| 22 <param name="allchroms" value="true" /> | |
| 23 <output name="output" file="gops_complement_out.bed" /> | |
| 24 </test> | |
| 25 <test> | |
| 26 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" /> | |
| 27 <param name="allchroms" value="true" /> | |
| 28 <output name="output" file="gops_complement_out_diffCols.dat" /> | |
| 29 </test> | |
| 30 <test> | |
| 31 <param name="input1" value="gops_bigint.interval" dbkey="hg17" /> | |
| 32 <param name="allchroms" value="true" /> | |
| 33 <output name="output" file="gops_complement_out2.bed" /> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help> | |
| 37 | |
| 38 .. class:: infomark | |
| 39 | |
| 40 **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. | |
| 41 | |
| 42 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. | |
| 43 | |
| 44 ----- | |
| 45 | |
| 46 **Screencasts!** | |
| 47 | |
| 48 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
| 49 | |
| 50 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
| 51 | |
| 52 ----- | |
| 53 | |
| 54 **Syntax** | |
| 55 | |
| 56 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset. | |
| 57 | |
| 58 ----- | |
| 59 | |
| 60 **Example** | |
| 61 | |
| 2 | 62 .. image:: gops_complement.gif |
| 0 | 63 |
| 64 </help> | |
| 65 </tool> |