Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/complement.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 1 <tool id="gops_complement_1" name="Complement"> | |
| 2 <description>intervals of a dataset</description> | |
| 3 <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> | |
| 4 <inputs> | |
| 5 <param format="interval" name="input1" type="data"> | |
| 6 <label>Complement regions of</label> | |
| 7 </param> | |
| 8 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement"> | |
| 9 </param> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data format="input" name="output" metadata_source="input1" /> | |
| 13 </outputs> | |
| 14 <code file="operation_filter.py"/> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="input1" value="1.bed" dbkey="?" /> | |
| 18 <param name="allchroms" value="true" /> | |
| 19 <output name="output" file="gops_complement_out.bed" /> | |
| 20 </test> | |
| 21 <test> | |
| 22 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="?" /> | |
| 23 <param name="allchroms" value="true" /> | |
| 24 <output name="output" file="gops_complement_out_diffCols.dat" /> | |
| 25 </test> | |
| 26 <test> | |
| 27 <param name="input1" value="gops_bigint.interval" dbkey="?" /> | |
| 28 <param name="allchroms" value="true" /> | |
| 29 <output name="output" file="gops_complement_out2.bed" /> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help> | |
| 33 | |
| 34 .. class:: infomark | |
| 35 | |
| 36 **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. | |
| 37 | |
| 38 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. | |
| 39 | |
| 40 ----- | |
| 41 | |
| 42 **Screencasts!** | |
| 43 | |
| 44 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
| 45 | |
| 46 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
| 47 | |
| 48 ----- | |
| 49 | |
| 50 **Syntax** | |
| 51 | |
| 52 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Example** | |
| 57 | |
| 58 .. image:: ./static/operation_icons/gops_complement.gif | |
| 59 | |
| 60 </help> | |
| 61 </tool> |