--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_annotate.xml	Sat Dec 10 21:13:10 2022 +0000
@@ -0,0 +1,201 @@
+<tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>metagenome-assembled-genomes (MAGs)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+
+## DRAM names the genbank output based on the input_fasta file name
+#set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0]
+#set output_gbk_file_name = $input_fasta_file_name + '.gbk'
+
+DRAM.py annotate
+--input_fasta '$input_fasta'
+--output_dir 'output_dir'
+--min_contig_size $min_contig_size
+--prodigal_mode '$prodigal_mode'
+--trans_table $trans_table
+--bit_score_threshold $bit_score_threshold
+--rbh_bit_score_threshold $rbh_bit_score_threshold
+$kofam_use_dbcan2_thresholds
+#if str($custom_fasta_dbs_cond.custom_dbs_fasta) == 'yes':
+    #for additional_db in $custom_fasta_dbs_cond.custom_fasta_dbs:
+        --custom_db_name '$additional_db.custom_db_name'
+        --custom_fasta_loc '$additional_db.custom_fasta_loc'
+    #end for
+#end if
+#if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes':
+    #for additional_db in $custom_hmm_dbs_cond.custom_hmm_dbs:
+        --custom_hmm_name '$additional_db.custom_hmm_name'
+        --custom_hmm_loc '$additional_db.custom_hmm_loc'
+        #if $additional_db.custom_hmm_cutoffs_loc:
+            --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc'
+        #end if
+    #end for
+#end if
+$use_uniref
+$use_vogdb
+$low_mem_mode
+$skip_trnascan
+--threads \${GALAXY_SLOTS:-10}
+&& test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced'
+&& test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced'
+&& test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced'
+&& test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced'
+&& test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced'
+&& test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced'
+&& test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced'
+&& test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced'
+    ]]></command>
+    <inputs>
+        <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/>
+        <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/>
+        <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length >3 Kbp)">
+            <option value="single" selected="true">single</option>
+            <option value="meta">meta</option>
+            <option value="train">train</option>
+        </param>
+        <param argument="--trans_table" type="integer" value="11" min="1" max="25" label="Translation table for prodigal to use for gene calling"/>
+        <param argument="--bit_score_threshold" type="integer" value="60" min="1" label="Minimum bitScore of search to retain hits"/>
+        <param argument="--rbh_bit_score_threshold" type="integer" value="350" min="1" label="Minimum bitScore of reverse best hits to retain hits"/>
+        <param argument="--kofam_use_dbcan2_thresholds" type="boolean" truevalue="--kofam_use_dbcan2_thresholds" falsevalue="" checked="false" label="Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs?"/>
+        <conditional name="custom_fasta_dbs_cond">
+            <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <repeat name="custom_fasta_dbs" title="FASTA file" min="1">
+                    <param argument="--custom_db_name" type="text" value="CF1" label="Custom FASTA database name">
+                        <validator type="empty_field"/>
+                        <expand macro="sanitizer"/>
+                    </param>
+                    <param argument="--custom_fasta_loc" type="data" format="fasta,fasta.gz" label="Custom database FASTA file"/>
+                </repeat>
+            </when>
+        </conditional>
+        <conditional name="custom_hmm_dbs_cond">
+            <param name="custom_dbs_hmm" type="select" label="Specify additional hmm files against which to annotate?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <repeat name="custom_hmm_dbs" title="HMM file" min="1">
+                    <param argument="--custom_hmm_name" type="text" value="CH1" label="Custom HMM database name">
+                        <validator type="empty_field"/>
+                        <expand macro="sanitizer"/>
+                    </param>
+                    <param argument="--custom_hmm_loc" type="data" format="hmm2,hmm3" label="Custom database HMM file"/>
+                    <param argument="--custom_hmm_cutoffs_loc" type="data" format="tabular,tsv" optional="true" label="Custom HMM cutoffs and descriptions file" help="Optional, leave blank to ignore"/>
+                </repeat>
+            </when>
+        </conditional>
+        <param argument="--use_uniref" type="boolean" truevalue="--use_uniref" falsevalue="" checked="false" label="Annotate the input FASTA files against UniRef?" help="Increases run time and memory requirements"/>
+        <param argument="--use_vogdb" type="boolean" truevalue="--use_vogdb" falsevalue="" checked="false" label="Annotate the input FASTA files against VOGDB?" help="Decreases run time"/>
+        <param argument="--low_mem_mode" type="boolean" truevalue="--low_mem_mode" falsevalue="" checked="false" label="Skip annotating with uniref and use kofam?" help="Decreases memory requirements"/>
+        <param argument="--skip_trnascan" type="boolean" truevalue="--skip_trnascan" falsevalue="" checked="false" label="Skip transcan"/>
+    </inputs>
+    <outputs>
+        <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/>
+        <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/>
+        <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/>
+        <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/>
+        <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"/>
+        <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"/>
+        <data name="output_genbank" format="genbank" label="${tool.name} on ${on_string}: genbank"/>
+        <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="8">
+            <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/>
+            <param name="prodigal_mode" value="meta"/>
+            <output name="output_genes_faa">
+                <assert_contents>
+                    <has_text text="rank"/>
+                </assert_contents>
+            </output>
+            <output name="output_genes_fna">
+                <assert_contents>
+                    <has_text text="rank"/>
+                </assert_contents>
+            </output>
+            <output name="output_genes_gff">
+                <assert_contents>
+                    <has_text text="gff-version 3"/>
+                </assert_contents>
+            </output>
+            <output name="output_scaffolds_fna">
+                <assert_contents>
+                    <has_text text="scaffold"/>
+                </assert_contents>
+            </output>
+            <output name="output_rrnas">
+                <assert_contents>
+                    <has_text text="scaffold"/>
+                </assert_contents>
+            </output>
+            <output name="output_trnas">
+                <assert_contents>
+                    <has_text text="fasta"/>
+                </assert_contents>
+            </output>
+            <output name="output_genbank">
+                <assert_contents>
+                    <has_text text="LOCUS"/>
+                </assert_contents>
+            </output>
+            <output name="output_annotations">
+                <assert_contents>
+                    <has_text text="fasta"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- These settings require a db which doesn't exist in the test environment -->
+        <test expect_failure="true">
+            <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/>
+            <param name="custom_dbs_fasta" value="yes"/>
+            <repeat name="custom_fasta_dbs">
+                <param name="custom_db_name" value="CF1"/>
+                <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/>
+            </repeat>
+            <param name="custom_dbs_hmm" value="yes"/>
+            <repeat name="custom_hmm_dbs">
+                <param name="custom_hmm_name" value="CH1"/>
+                <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/>
+            </repeat>
+            <param name="prodigal_mode" value="meta"/>
+            <assert_stderr>
+                <has_text text="returned non-zero exit status"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+@WHATITDOESHEADER@
+
+This tool annotates genes by assigning database identifiers to them.  Short contigs (default less than 2,500 bp) are initially
+removed  and then Prodigal is used to detect open reading frames (ORFs) and to predict their amino acid sequences.  Next, DRAM
+searches all amino acid sequences against multiple databases, providing a single Raw output.  When gene annotation is complete,
+all results are merged in a single tabular annotation table, including the best hit for each database, for user comparison.
+
+This tool accepts assembly-derived fastA files which may come from unbinned data (metagenome contig or scaffold files) or
+genome-resolved data from one or many organisms (isolate genomes, single-amplified genome (SAGs), MAGs).
+
+This tool produces the following outputs.
+
+ * A tabular file with all annotations from Pfam, UniProt, dbCAN and MEROPS databases for all genes in the input genomes
+ * Genbank files for each genome
+ * A gff file of all annotations across genomes
+ * A fasta file of each open reading frame amino acid sequence and best ranked annotation
+ * Tabular files with tRNAs and rRNAs
+
+@WHATITDOESFOOTER@
+    </help>
+    <expand macro="citations"/>
+</tool>