<tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>around genes of interest</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <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>