--- a/bam_readtagger.xml	Fri Feb 17 12:55:58 2017 -0500
+++ b/bam_readtagger.xml	Tue Feb 21 04:39:31 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.1.13">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.2.0">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.1.13">readtagger</requirement>
+        <requirement type="package" version="0.2.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
@@ -15,6 +15,7 @@
         $keep_suboptimal
         $discarded
         $verified
+        $discard_proper_pairs
         -o '$tagged_file'
     ]]></command>
     <inputs>
@@ -30,6 +31,7 @@
         </repeat>
         <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
         <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/>
+        <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/>
         <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
         <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
     </inputs>
@@ -69,24 +71,62 @@
             <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
             <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
         </test>
+        <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
+            <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
+            <repeat name="alignment_series">
+                <param name="annotate_with" value="proper_pair_discard_fbti.bam" ftype="bam"/>
+                <param name="r_tag" value="A"/>
+                <param name="m_tag" value="B"/>
+            </repeat>
+            <param name="discarded" value="True"/>
+            <param name="keep_suboptimal" value="True"/>
+            <param name="discard_proper_pairs" value="True"/>
+            <param name="verified" value="True"/>
+            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" />
+            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/>
+            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/>
+        </test>
     </tests>
     <help><![CDATA[
-        usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
-                 OUTPUT_FILE
+.. code-block::
 
-Tag reads in an alignment file based on other alignment files
+    usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
+                      OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED]
+                      [-wv WRITE_VERIFIED] [--version]
+
+    Tag reads in an alignment file based on other alignment files
 
-optional arguments:
-  -h, --help            show this help message and exit
-  -t TAG_FILE, --tag_file TAG_FILE
-                        Tag reads in this file. (default: None)
-  -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
-                        Tag reads in readfile if reads are aligned in these
-                        files.Append `:A:B` to tag first letter of tag
-                        describing read as A, and first letter of tag
-                        describing the mate as B (default: None)
-  -o OUTPUT_FILE, --output_file OUTPUT_FILE
-                        Write bam file to this path (default: None)
+    optional arguments:
+      -h, --help            show this help message and exit
+      -t TAG_FILE, --tag_file TAG_FILE
+                            Tag reads in this file. (default: None)
+      -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
+                            Tag reads in readfile if reads are aligned in these
+                            files.Append `:A:B` to tag first letter of tag
+                            describing read as A, and first letter of tag
+                            describing the mate as B (default: None)
+      -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                            Write bam file to this path (default: None)
+      -d, --allow_dovetailing
+                            Sets the proper pair flag (0x0002) to true if reads
+                            dovetail [reads reach into or surpass the mate
+                            sequence]. (default: False)
+      -dp, --discard_if_proper_pair
+                            Discard an alternative flag if the current read is in
+                            a proper pair. (default: False)
+      -k, --keep_suboptimal_alternate_tags
+                            By default cigarstrings of the alternative tags are
+                            compared and alternates that are not explaining the
+                            current cigar strings are discarded. Use this option
+                            to keep the alternative tags (effectively restoring
+                            the behaviour of readtagger < 0.1.4) (default: False)
+      -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED
+                            Write discarded reads into separate file (default:
+                            False)
+      -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED
+                            Write verified reads into separate file (default:
+                            False)
+      --version             show program's version number and exit
 
     ]]></help>
 </tool>