--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/naive_variant_caller.xml	Thu Aug 29 10:54:14 2013 -0400
@@ -0,0 +1,208 @@
+<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.1">
+  <description> - tabulate variable sites from BAM datasets</description>
+  <requirements>
+    <requirement type="package" version="1.7.1">numpy</requirement>
+    <requirement type="package" version="0.0.1">pyBamParser</requirement>
+    <requirement type="package" version="0.0.1">pyBamTools</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" err_level="fatal" />
+    <exit_code range=":-1" err_level="fatal" />
+  </stdio>
+  <command interpreter="python">naive_variant_caller.py
+      -o "${output_vcf}"
+     
+     #for $input_bam in $reference_source.input_bams:
+         -b "${input_bam.input_bam}"
+         -i "${input_bam.input_bam.metadata.bam_index}"
+     #end for
+     
+     #if $reference_source.reference_source_selector != "history":
+         -r "${reference_source.ref_file.fields.path}"
+     #elif $reference_source.ref_file:
+         -r "${reference_source.ref_file}"
+     #end if
+     
+     #for $region in $regions:
+         --region "${region.chromosome}:${region.start}-${region.end}"
+     #end for
+     
+     ${variants_only}
+     
+     ${use_strand}
+     
+     --ploidy "${$ploidy}"
+     
+     --min_support_depth "${min_support_depth}"
+     
+     #if str($min_base_quality):
+         --min_base_quality "${min_base_quality}"
+     #end if
+     
+     #if str($min_mapping_quality):
+         --min_mapping_quality "${min_mapping_quality}"
+     #end if
+     
+     --coverage_dtype "${coverage_dtype}"
+     
+     --allow_out_of_bounds_positions
+     
+  </command>
+  <inputs>
+    <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">
+        <repeat name="input_bams" title="BAM file" min="1" >
+            <param name="input_bam" type="data" format="bam" label="BAM file">
+              <validator type="unspecified_build" />
+              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+            </param>
+        </repeat>
+        <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="dbkey"/> does not yet work in a repeat...--> 
+          </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!!!! -->
+        <repeat name="input_bams" title="BAM file" min="1" >
+            <param name="input_bam" type="data" format="bam" label="BAM file" >
+            </param>
+        </repeat>
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" optional="True" />
+      </when>
+    </conditional>
+
+    <repeat name="regions" title="Restrict to regions" min="0" >
+        <param name="chromosome" type="text" value="" optional="False" label="Chromosome" />
+        <param name="start" type="integer" value="" optional="True" label="Start" />
+        <param name="end" type="integer" value="" optional="True" label="End" />
+    </repeat>
+
+    <!-- TODO: enhance filtering -->
+    <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
+    <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
+    <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
+    
+    <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
+    <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
+    
+    <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
+    
+    <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
+      <option value="uint8">uint8</option>
+      <option value="uint16" selected="True">uint16</option>
+      <option value="uint32">uint32</option>
+      <option value="uint64">uint64</option>
+    </param>
+    
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output_vcf" />
+  </outputs>
+  <help>
+**What it does**
+
+This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples. 
+
+User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately. 
+
+In addition to calling alternate alleles based upon simple ratios of nucleotides at a position, per base nucleotide counts are also provided. A custom tag, NC, is used within the Genotype fields. The NC field is a comma-separated listing of nucleotide counts in the form of &lt;nucleotide&gt;=&lt;count&gt;, where a plus or minus character is prepended to indicate strand, if the strandedness option was specified.
+ 
+
+------
+
+**Inputs**
+
+Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
+
+
+**Outputs**
+
+The output is in VCF format.
+
+Example VCF output line, without reporting by strand:
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
+
+Example VCF output line, when reporting by strand:
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
+
+**Options**
+
+Reference Genome:
+
+    Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
+
+Restrict to regions:
+
+    You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
+
+Minimum number of reads needed to consider a REF/ALT:
+
+    This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
+
+Minimum base quality:
+
+    The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
+
+Minimum mapping quality:
+
+    The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
+
+Ploidy:
+
+    The number of genotype calls to make at each reported position.
+
+Only write out positions with with possible alternate alleles:
+
+    When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
+
+Report counts by strand:
+
+    When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
+
+Choose the dtype to use for storing coverage information:
+
+    This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
+
+        +--------+----------------------------+
+        | name   | maximum coverage value     |
+        +========+============================+
+        | uint8  | 255                        |
+        +--------+----------------------------+
+        | uint16 | 65,535                     |
+        +--------+----------------------------+
+        | uint32 | 4,294,967,295              |
+        +--------+----------------------------+
+        | uint64 | 18,446,744,073,709,551,615 |
+        +--------+----------------------------+
+
+------
+
+**Citation**
+
+If you use this tool, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" /> 
+          <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
+          <param name="regions" value="0" />
+          <param name="min_support_depth" value="0" />
+          <param name="min_base_quality" value="" />
+          <param name="min_mapping_quality" value="" />
+          <param name="ploidy" value="2" />
+          <param name="variants_only" value="False" />
+          <param name="use_strand" value="False" />
+          <param name="coverage_dtype" value="uint8" />
+          <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
+      </test>
+  </tests>
+  
+</tool>