--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_neighborhoods.xml	Sat Dec 10 21:14:08 2022 +0000
@@ -0,0 +1,121 @@
+<tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>around genes of interest</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+DRAM.py neighborhoods
+--input_file '$input_file'
+--output_dir 'output_dir'
+#if $advanced.genes:
+    --genes '$advanced.genes'
+#end if
+#if $advanced.identifiers:
+    --identifiers '$advanced.identifiers'
+#end if
+#if $advanced.custom_distillate:
+    --custom_distillate '$advanced.custom_distillate'
+#end if
+## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
+##if $advanced.categories:
+##    --categories '$advanced.categories'
+##end if
+#if $advanced.genes_loc:
+    --genes_loc '$advanced.genes_loc'
+#end if
+#if $advanced.scaffolds_loc:
+    --scaffolds_loc '$advanced.scaffolds_loc'
+#end if
+#if $advanced.distance_genes > 0:
+    --distance_genes $advanced.distance_genes
+#end if
+#if $advanced.distance_bp > 0:
+    --distance_bp $advanced.distance_bp
+#end if
+&& test -f 'output_dir/neighborhood_annotations.tsv' && mv 'output_dir/neighborhood_annotations.tsv' '$output_neighborhood_annotations' || echo 'No neighborhood_annotations.tsv output produced'
+#if $advanced.genes_loc:
+    && test -f 'output_dir/neighborhood_genes.dat' && mv 'output_dir/neighborhood_genes.dat' '$output_neighborhood_genes' || echo 'No neighborhood_genes.dat output produced'
+#end if
+#if $advanced.scaffolds_loc:
+    && test -f 'output_dir/neighborhood_scaffolds.fna' && mv 'output_dir/neighborhood_scaffolds.fna' '$output_neighborhood_scaffolds' || echo 'No neighborhood_scaffolds.fna output produced'
+#end if
+    ]]></command>
+    <inputs>
+        <expand macro="input_file_param"/>
+        <section name="advanced" title="Advanced options" expanded="false">
+            <expand macro="genes_param"/>
+            <expand macro="identifiers_param"/>
+            <expand macro="custom_distillate_param"/>
+            <!-- Broken in 3.5.1 - see above -->
+            <!-- <expand macro="categories_param"/> -->
+            <param argument="--genes_loc" type="data" format="fasta" optional="true" label="File containing genes to filter to neighborhoods" help="Optional, leave blank to ignore"/>
+            <param argument="--scaffolds_loc" type="data" format="fasta" optional="true" label="File containing scaffolds to filter to neighborhoods" help="Optional, leave blank to ignore"/>
+            <param argument="--distance_genes" type="integer" value="0" min="0" label="Number of genes away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in genes, bp or both"/>
+            <param argument="--distance_bp" type="integer" value="0" min="0" label="Number of base pairs away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in bp, genes or both"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_neighborhood_annotations" format="tabular" label="${tool.name} on ${on_string}: neighborhood annotations"/>
+        <data name="output_neighborhood_genes" format="fasta" label="${tool.name} on ${on_string}: neighborhood genes">
+            <filter>advanced['genes_loc']</filter>
+        </data>
+        <data name="output_neighborhood_scaffolds" format="fasta" label="${tool.name} on ${on_string}: neighborhood scaffolds">
+            <filter>advanced['scaffolds_loc']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
+            <param name="distance_genes" value="10"/>
+            <output name="output_neighborhood_annotations">
+                <assert_contents>
+                    <has_size value="2046495" delta="1000"/>
+                </assert_contents>
+                <assert_contents>
+                    <has_text text="neighborhood_number"/>
+                </assert_contents>
+            </output>
+       </test>
+        <test expect_num_outputs="3">
+            <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
+            <param name="distance_genes" value="10"/>
+            <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
+            <param name="genes_loc" ftype="fasta" value="neighborhoods_genes_loc1.fna"/>
+            <param name="scaffolds_loc" ftype="fasta" value="neighborhoods_scaffolds_loc1.fasta"/>
+            <output name="output_neighborhood_annotations">
+                <assert_contents>
+                    <has_size value="2046495" delta="10000"/>
+                </assert_contents>
+                <assert_contents>
+                    <has_text text="neighborhood_number"/>
+                </assert_contents>
+            </output>
+            <output name="output_neighborhood_genes" ftype="fasta" value="neighborhoods_output1.fasta"/>
+            <output name="output_neighborhood_scaffolds" ftype="fasta" value="neighborhoods_output1.fasta">
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+@WHATITDOESHEADER@
+
+This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
+DRAM annotate tool and finds neighborhoods around genes of interest.
+
+@CUSTOMDISTILLATEFILES@
+
+**Options**
+
+ * **Space-separated list of genes to keep** - genee names from DRAM around which to find neighborhoods
+ * **Database identifiers** - database identifiers assigned by DRAM around which to find neighborhoods
+ * **File containing genes to filter to neighborhoods** - file containing genes to filter to neighborhoods
+ * **File containing scaffolds to filter to neighborhoods** - file containing scaffolds to filter to neighborhoods
+ * **Number of genes away from center to include in neighborhoods** - number of genes away from center to include in neighborhoods
+ * **Number of base pairs away from center to include in neighborhoods** - number of base pairs away from center to include in neighborhoods
+
+@WHATITDOESFOOTER@
+    </help>
+    <expand macro="citations"/>
+</tool>