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1 <tool id="gops_complement_1" name="Complement" version="0.0.1">
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2 <description>intervals of a dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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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>
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8 <inputs>
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9 <param format="interval" name="input1" type="data">
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10 <label>Complement regions of</label>
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11 </param>
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12 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="input" name="output" metadata_source="input1" />
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17 </outputs>
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18 <code file="operation_filter.py"/>
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19 <tests>
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20 <test>
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21 <param name="input1" value="1.bed" dbkey="hg17" />
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22 <param name="allchroms" value="true" />
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23 <output name="output" file="gops_complement_out.bed" />
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24 </test>
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25 <test>
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26 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
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27 <param name="allchroms" value="true" />
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28 <output name="output" file="gops_complement_out_diffCols.dat" />
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29 </test>
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30 <test>
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31 <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
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32 <param name="allchroms" value="true" />
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33 <output name="output" file="gops_complement_out2.bed" />
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34 </test>
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35 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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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.
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41
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42 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval.
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43
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44 -----
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45
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46 **Screencasts!**
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47
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48 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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49
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50 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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51
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52 -----
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53
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54 **Syntax**
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55
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56 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset.
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57
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58 -----
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59
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60 **Example**
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61
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62 .. image:: ${static_path}/operation_icons/gops_complement.gif
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63
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64 </help>
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65 </tool>
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