Mercurial > repos > devteam > bamtools_filter
comparison bamtools-filter.xml @ 2:39e21f756379 draft
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 15:03:33 -0400 |
| parents | 5e2fe70292a7 |
| children | 07d099ccd10f |
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| 1:5e2fe70292a7 | 2:39e21f756379 |
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| 244 **Example 1. Using a single filter** | 244 **Example 1. Using a single filter** |
| 245 | 245 |
| 246 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters). | 246 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters). |
| 247 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: | 247 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: |
| 248 | 248 |
| 249 .. image:: images/single-filter.png | 249 .. image:: ${static_path}/images/single-filter.png |
| 250 | 250 |
| 251 ----- | 251 ----- |
| 252 | 252 |
| 253 **Example 2. Using multiple filters** | 253 **Example 2. Using multiple filters** |
| 254 | 254 |
| 255 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only. | 255 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only. |
| 256 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button): | 256 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button): |
| 257 | 257 |
| 258 .. image:: images/multiple-filters.png | 258 .. image:: ${static_path}/images/multiple-filters.png |
| 259 | 259 |
| 260 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering. | 260 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering. |
| 261 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example. | 261 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example. |
| 262 | 262 |
| 263 ----- | 263 ----- |
| 266 | 266 |
| 267 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) | 267 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) |
| 268 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. | 268 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. |
| 269 The following screenshot expalins how this can be done: | 269 The following screenshot expalins how this can be done: |
| 270 | 270 |
| 271 .. image:: images/complex-filters.png | 271 .. image:: ${static_path}/images/complex-filters.png |
| 272 | 272 |
| 273 ----- | 273 ----- |
| 274 | 274 |
| 275 **Example 4. Even more complex filtering with Rules** | 275 **Example 4. Even more complex filtering with Rules** |
| 276 | 276 |
| 280 | 280 |
| 281 !(1) & (2 | 3) | 281 !(1) & (2 | 3) |
| 282 | 282 |
| 283 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: | 283 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: |
| 284 | 284 |
| 285 .. image:: images/rule.png | 285 .. image:: ${static_path}/images/rule.png |
| 286 | 286 |
| 287 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule. | 287 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule. |
| 288 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means:: | 288 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means:: |
| 289 | 289 |
| 290 NOT condition 1 AND (condition 2 OR condition 3) | 290 NOT condition 1 AND (condition 2 OR condition 3) |