--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools.xml	Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,293 @@
+<?xml version="1.0"?>
+<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1">
+  <description>BAM datasets and perform other transformations</description>
+  <requirements>
+    <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  
+  <command>
+   ##set up input files
+  
+  #for $bam_count, $input_bam in enumerate( $input_bams ):
+    ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
+    ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
+  #end for
+   
+  #if str( $analysis_type.analysis_type_selector ) == "convert":
+    #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+      #set $reference_fasta_filename = "localref.fa"
+      #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
+        ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for bamtools convert" &gt;&amp;2 &amp;&amp;
+      #else:
+        #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
+      #end if
+    #end if
+  #end if
+
+    ##finished setting up inputs
+    
+    ##start bamtools commandline
+    
+    bamtools
+    
+    #if str( $analysis_type.analysis_type_selector ) == "convert":
+    
+    convert
+    
+    -format ${analysis_type.format_type.format_type_selector}
+    
+      #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+    
+      ${analysis_type.format_type.mapqual}
+      -fasta "${reference_fasta_filename}"
+    
+      #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
+    
+      ${analysis_type.format_type.noheader}
+    
+      #end if
+      
+    -out $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "count":
+    
+    count
+    > $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "coverage":
+    
+    coverage
+    -out $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "header":
+    
+    header
+    > $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "merge":
+    
+    merge
+    -out $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "random":
+    
+    random
+    -n ${analysis_type.count}
+    -seed ${analysis_type.seed}
+    -out $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "revert":
+    
+    revert
+    ${analysis_type.keepDuplicate}
+    ${analysis_type.keepQualities}
+    -out $out_file1
+    
+    #elif str( $analysis_type.analysis_type_selector ) == "sort":
+    
+    sort
+    ${analysis_type.byname}
+    -out $out_file1
+    
+    #end if
+    
+    #for $bam_count, $input_bam in enumerate( $input_bams ):
+        -in "localbam_${bam_count}.bam"
+    #end for
+    
+   
+  </command>
+  <inputs>
+    
+    <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
+          <param name="input_bam" type="data" format="bam" label="BAM dataset" />
+    </repeat>
+
+    <conditional name="analysis_type">
+      <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
+        <option value="convert">Convert</option>
+        <option value="count">Count</option>
+        <option value="coverage">Coverage</option>
+        <option value="header">Header</option>
+        <option value="merge">Merge</option>
+        <option value="random">Random</option>
+        <option value="revert">Revert</option>
+      <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
+      <!-- Allowing users for sort files may break donstream functionality. -->
+      <!-- To enable sort option simply uncomment the line below: -->
+      <!--  <option value="sort">Sort</option> -->
+      </param>
+      <when value="convert">
+        <conditional name="format_type">
+          <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
+           <option value="bed">BED</option>
+           <option value="fasta">FASTA</option>
+           <option value="fastq">FASTQ</option>
+           <option value="json">JSON</option>
+           <option value="pileup">Pileup</option>
+           <option value="sam">SAM</option>
+           <option value="yaml">YAML</option>
+          </param>
+          <when value="pileup">
+            <conditional name="reference_source">
+              <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+              </param>
+              <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome">
+                  <options from_data_table="sam_fa_indexes">
+                  <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
+                  </options>
+                  <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+              </when>
+              <when value="history"> <!-- FIX ME!!!! -->
+                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+              </when>
+            </conditional>
+            <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
+          </when>
+          <when value="sam">
+            <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
+          </when>
+        </conditional>
+      </when>
+      <when value="count">
+      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
+      </when>
+      <when value="coverage">
+      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
+      </when>
+      <when value="header">
+      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
+      </when>
+      <when value="merge">
+      <!-- Nothing to be done with count -> just count alignments in the input bam(s) -->
+      </when>
+      <when value="random">
+        <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
+        <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
+      </when>
+      <when value="revert">
+        <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
+        <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
+      </when>
+      <when value="sort">
+        <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
+      </when>
+    </conditional>
+    
+    </inputs>
+    <outputs>
+      <data format="txt" name="out_file1">
+        <change_format>
+          <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
+          <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
+          <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
+          <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
+          <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
+          <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
+          <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
+          <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
+          <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
+          <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
+        </change_format>
+      </data>  
+    </outputs>
+    <tests>
+      <test>
+        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="analysis_type_selector" value="convert"/>
+        <param name="format_type_selector" value="pileup"/>
+        <param name="reference_source_selector" value="history" />
+        <param name="mapqual" value="true" />
+        <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
+        <output name="output_bam" file="bamtools-convert-pileup.pu" />
+      </test>
+      <test>
+        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="analysis_type_selector" value="count"/>
+        <output name="output_bam" file="bamtools-count.tab" />
+      </test>
+      <test>
+        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="analysis_type_selector" value="coverage"/>
+        <output name="output_bam" file="bamtools-coverage.tab" />
+      </test>
+      <test>
+        <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+        <param name="analysis_type_selector" value="header"/>
+        <output name="output_bam" file="bamtools-header.txt" />
+      </test>
+    </tests>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  
+  <help>
+
+**What is does**
+
+BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
+This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.
+
+-----
+
+**Convert**
+
+Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
+cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
+
+-----
+
+**Count**
+
+Counts a number of alignments in a BAM dataset(s).
+
+-----
+
+**Coverage**
+
+Prints per-base coverage for a BAM dataset.
+
+-----
+
+**Header**
+
+Prints header from a BAM dataset(s).
+
+------
+
+**Merge**
+
+Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.
+
+------
+
+**Random**
+
+Grabs a specified number of random lines from BAM dataset(s).
+
+------
+
+**Revert**
+
+Removes duplicate marks and restores original (non-recalibrated) base qualities.
+
+-----
+
+.. class:: infomark
+
+**More information**
+
+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
+
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btr174</citation>
+  </citations>
+</tool>