diff bamtools-filter.xml @ 5:23a1c1f66b47 draft

planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty

--- a/bamtools-filter.xml	Wed Aug 26 15:11:21 2015 -0400
+++ b/bamtools-filter.xml	Wed Aug 26 15:12:16 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}/single-filter.png
+.. image:: 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}/multiple-filters.png
+.. image:: 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}/complex-filters.png
+.. image:: 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}/rule.png
+.. image:: 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::