--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_readtagger.xml	Fri Feb 17 10:54:47 2017 -0500
@@ -0,0 +1,92 @@
+<tool id="bam_readtagger" name="Tag alignment files" version="0.1.8">
+    <description>from multiple bam files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="0.1.8">readtagger</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        readtagger -t '$tag_file' -a
+        #for $element in $alignment_series
+            '$element.annotate_with':$element.r_tag:$element.m_tag
+        #end for
+        $allow_dovetailing
+        $keep_suboptimal
+        $discarded
+        $verified
+        -o '$tagged_file'
+    ]]></command>
+    <inputs>
+        <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
+        <repeat name="alignment_series" title="Alignments">
+            <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
+            <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
+                <expand macro="tag_options"/>
+            </param>
+            <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
+                <expand macro="tag_options"/>
+            </param>
+        </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="-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>
+    <outputs>
+        <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
+        <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
+            <filter>verified is True</filter>
+        </data>
+        <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string">
+            <filter>verified is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) -->
+            <param name="tag_file" value="dm6.bam" ftype="bam"/>
+            <repeat name="alignment_series">
+                <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/>
+                <param name="r_tag" value="A"/>
+                <param name="m_tag" value="B"/>
+            </repeat>
+            <param name="discarded" value="True"/>
+            <param name="verified" value="True"/>
+            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
+            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
+            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
+        </test>
+        <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
+            <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
+            <repeat name="alignment_series">
+                <param name="annotate_with" value="dm6.bam" ftype="bam"/>
+                <param name="r_tag" value="A"/>
+                <param name="m_tag" value="B"/>
+            </repeat>
+            <param name="discarded" value="True"/>
+            <param name="verified" value="True"/>
+            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
+            <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>
+    </tests>
+    <help><![CDATA[
+        usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
+                 OUTPUT_FILE
+
+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)
+
+    ]]></help>
+</tool>