--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tb_variant_filter.xml	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,160 @@
+<tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04">
+    <description>M. tuberculosis H37Rv VCF filter</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.3</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        tb_variant_filter
+        #if "region_filter" in str($filters).split(',')
+            #if str($filter_options.show_filter_options) == "yes":
+                --region_filter $filter_options.region_filter
+            #else
+                --region_filter pe_ppe,uvp
+            #end if
+        #end if
+        #if "close_to_indel_filter" in str($filters).split(',')
+            --close_to_indel_filter
+            #if str($filter_options.show_filter_options) == "yes":
+                --indel_window_size $filter_options.indel_window_size
+            #end if
+        #end if
+        #if "min_percentage_alt_filter" in str($filters).split(',') 
+            --min_percentage_alt_filter 
+            #if str($filter_options.show_filter_options) == "yes":
+                --min_percentage_alt $filter_options.min_percentage_alt
+            #end if
+        #end if
+        #if "min_depth_filter" in str($filters).split(',') 
+            --min_depth_filter 
+            #if str($filter_options.show_filter_options) == "yes":
+                --min_depth $filter_options.min_depth
+            #end if
+        #end if
+        #if "snv_only_filter" in str($filters).split(','):
+            --snv_only_filter
+        #end if
+        '$input1' '$output1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" label="VCF file to be filter"  format="vcf"/>
+
+        <param type="select" name="filters" multiple="true" label="Filters to apply">
+            <option value="region_filter" selected="true">Filter out variants by regions</option>
+            <option value="close_to_indel_filter">Filter variants close to indels</option>
+            <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option>
+            <option value="min_depth_filter">Filter sites by read alignment depth</option>
+            <option value="snv_only_filter">Only accept SNVs</option>
+        </param>
+
+        <conditional name="filter_options">
+            <param type="select" name="show_filter_options" label="Show options for the filters">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable">
+                    <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here -->
+                    <option value="pe_ppe" selected="true">PE/PPE</option>
+                    <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
+                    <option value="mtbseq">MTBseq antibiotic resistant genes</option>
+                    <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option>
+                </param>
+                <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/>
+                <param argument="--min_percentage_alt" type="float" value="90"
+                    label="Minimum alternate allele percentage to accept"/>
+                <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/>
+            </when>
+            <when value="no"></when>
+
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="region_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="region_filter" value="pe_ppe,tbprofiler,uvp" />
+            </conditional>
+            <output name="output1" file="test_output1.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="close_to_indel_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="indel_window_size" value="5" />
+            </conditional>
+            <output name="output1" file="test_output2.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="min_percentage_alt_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_percentage_alt" value="95.0" />
+            </conditional>
+            <output name="output1" file="test_output3.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input2.vcf" ftype="vcf" />
+            <param name="filters" value="min_percentage_alt_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_percentage_alt" value="30.0" />
+            </conditional>
+            <output name="output1" file="test_output4.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="min_depth_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_depth" value="30" />
+            </conditional>
+            <output name="output1" file="test_output5.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="snv_only_filter" />
+            <output name="output1" file="test_output6.vcf" ftype="vcf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool offers multiple options for filtering variants (in
+VCF files, relative to M. tuberculosis H37Rv).
+
+It currently has 5 main modes:
+
+1. Filter by region. Mask out variants in certain regions. Region lists available as:
+    1.  PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
+    2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
+    3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
+    4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
+2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
+3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
+4. Filter by depth of aligned reads.
+5. Filter out all variants that are not SNV (single nucleotide variants).
+
+When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters).
+    ]]></help>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+@misc{vanHeusden2019,
+  author = {van Heusden, P.},
+  title = {tb_variant_filter},
+  year = {2019},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}},
+  commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c}
+}
+        ]]></citation>
+    </citations>
+</tool>