# HG changeset patch
# User devteam
# Date 1429643145 14400
# Node ID 8c34727900200419e42f812456b838031ee7adb3
# Parent  c04bee391baad824c4843e7dc66fda0cc7580163
Uploaded

diff -r c04bee391baa -r 8c3472790020 macros.xml
--- a/macros.xml	Wed Mar 18 16:43:50 2015 -0400
+++ b/macros.xml	Tue Apr 21 15:05:45 2015 -0400
@@ -7,7 +7,37 @@
     </xml>
     <xml name="citations">
         <citations>
+            <citation type="bibtex">
+                @misc{SAM_def,
+                title={Definition of SAM/BAM format},
+                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+            </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </citation>
         </citations>
     </xml>
     <xml name="version_command">
@@ -18,4 +48,23 @@
             <exit_code range="1:" level="fatal" description="Error" />
         </stdio>
     </xml>
+    <token name="@no-chrom-options@">
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
+
+    </token>
+
 </macros>
diff -r c04bee391baa -r 8c3472790020 samtools_bedcov.xml
--- a/samtools_bedcov.xml	Wed Mar 18 16:43:50 2015 -0400
+++ b/samtools_bedcov.xml	Tue Apr 21 15:05:45 2015 -0400
@@ -1,11 +1,11 @@
-<tool id="samtools_bedcov" name="Calculate read depth" version="1.0.1">
-  <description>on BAM files</description>
+<tool id="samtools_bedcov" name="BedCov" version="2.0">
+  <description>calculate read depth for a set of genomic intervals</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
     <expand macro="version_command"></expand>
-    <expand macro="stdio"></expand>
     <command><![CDATA[
         for bamfile in 
         #for dataset in $input_bams:
@@ -47,9 +47,9 @@
     <help>
 **What it does**
 
-This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
+Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
 
-Show read depth per BED region.
+ samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
 
     </help>
     <expand macro="citations"></expand>