# HG changeset patch
# User jbrayet
# Date 1448439729 18000
# Node ID 8be7fb96589d1b6a176868ee89d92ef39ead2311
# Parent  695b40cab89b158b7ba95864a1a3d0be0e408460
Uploaded

diff -r 695b40cab89b -r 8be7fb96589d samtools_calmd.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_calmd.xml	Wed Nov 25 03:22:09 2015 -0500
@@ -0,0 +1,99 @@
+<tool id="samtools_calmd" name="CalMD" version="2.0">
+  <description>recalculate MD/NM tags</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+    <command><![CDATA[
+        #if str( $reference_source.reference_source_selector ) == "history":
+            #set ref_fa = 'ref.fa'
+            ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
+        #else:
+            #set ref_fa = str( $reference_source.ref_fasta.fields.path )
+        #end if
+        samtools calmd
+        #if str($option_set.option_sets) == 'advanced':
+            $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
+        #end if
+        -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
+    </command>
+    <inputs>
+        <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_fasta" type="select" label="Using reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" column="0" key="dbkey" ref="input_bam" />
+                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
+            </when>
+        </conditional>
+        <conditional name="option_set">
+            <param name="option_sets" type="select" label="Options">
+                <option value="default">Use defaults</option>
+                <option value="advanced">Advanced options</option>
+            </param>
+            <when value="default" />
+            <when value="advanced">
+                <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/>
+                <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/>
+                <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/>
+                <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="option_sets" value="default" /> 
+            <param name="input_bam" value="phiX.bam"/>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_fasta" value="phiX.fasta" />
+            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
+        </test>
+        <test>
+            <param name="option_sets" value="advanced" /> 
+            <param name="change_identical" value="true" />
+            <param name="extended_baq" value="true" />
+            <param name="input_bam" value="phiX.bam"/>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_fasta" value="phiX.fasta" />
+            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options::
+
+  -e       change identical bases to '='
+  -A       modify the quality string
+  -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)
+  -E       extended BAQ for better sensitivity but lower specificity
+  
+-----
+
+**NM and MD tags**
+
+From SAM format specification::
+
+  MD (string)  String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
+  NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
+  
+See refernces for more information about SAM format tags.
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>