Mercurial > repos > devteam > samtools_bedcov

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 13 12:54:07 2015 -0400
@@ -0,0 +1,70 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </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">
+        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <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>
--- a/samtools_bedcov.xml	Mon Oct 27 12:42:42 2014 -0400
+++ b/samtools_bedcov.xml	Tue Oct 13 12:54:07 2015 -0400
@@ -1,9 +1,11 @@
-<tool id="samtools_bedcov" name="Calculate read depth" version="1.0.0">
-    <description>on BAM files</description>
-    <requirements>
-        <requirement type="package" version="1.1">samtools</requirement>
-    </requirements>
-    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+<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>
     <command><![CDATA[
         for bamfile in
         #for dataset in $input_bams:
@@ -21,10 +23,8 @@
             `basename "${dataset}"`
         #end for
         > "${output}"
-        ]]></command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
+        ]]>
+    </command>
     <inputs>
         <param name="input_bed" type="data" format="bed" label="BED file" />
         <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
@@ -47,16 +47,11 @@
     <help>
 **What it does**

-This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
-
-Show read depth per BED region.
-
-**Citation**
+Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::

-For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
-
+ samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]

-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
     </help>
+    <expand macro="citations"></expand>
 </tool>
--- a/tool_dependencies.xml	Mon Oct 27 12:42:42 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 12:54:07 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="1.1">
-        <repository changeset_revision="c01b111a243b" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>