Mercurial > repos > devteam > bamtools_filter
changeset 3:07d099ccd10f draft
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 15:04:36 -0400 |
| parents | 39e21f756379 |
| children | baca6d3e27af |
| files | bamtools-filter.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/bamtools-filter.xml Wed Aug 26 15:03:33 2015 -0400 +++ b/bamtools-filter.xml Wed Aug 26 15:04:36 2015 -0400 @@ -246,7 +246,7 @@ 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). For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: -.. image:: ${static_path}/images/single-filter.png +.. image:: ${static_path}images/single-filter.png ----- @@ -255,7 +255,7 @@ 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. 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): -.. image:: ${static_path}/images/multiple-filters.png +.. image:: ${static_path}images/multiple-filters.png 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. 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. @@ -268,7 +268,7 @@ 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*. The following screenshot expalins how this can be done: -.. image:: ${static_path}/images/complex-filters.png +.. image:: ${static_path}images/complex-filters.png ----- @@ -282,7 +282,7 @@ Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: -.. image:: ${static_path}/images/rule.png +.. image:: ${static_path}images/rule.png 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. 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::