# HG changeset patch
# User estrain
# Date 1603422076 14400
# Node ID b01213db5b81673fb7fd43a09121af1c55b2f6d0
# Parent  48124b139de71286f73679fbcd54673f05943f9c
Uploaded

diff -r 48124b139de7 -r b01213db5b81 amrfinder.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amrfinder.xml	Thu Oct 22 23:01:16 2020 -0400
@@ -0,0 +1,158 @@
+<tool id="amrfinder_gt" name="amrfinder_gt" version="@VERSION@+galaxy1">
+    <description>
+      identifies AMR genes using either protein annotations or nucleotide sequence.
+    </description>
+    <macros>
+        <token name="@VERSION@">3.8.28</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement>
+    </requirements>
+    <version_command><![CDATA[amrfinder --version]]></version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+    amrfinder
+    $plus
+    --threads \${GALAXY_SLOTS:-1}
+    --database '$amrfinder_databases.fields.path'
+    #if $input_selection.input_source_selector == 'nuc'
+        -n '$input_selection.fasta_file'
+    #elif  $input_selection.input_source_selector == 'pro'
+        -p '$input_selection.fasta_file'
+        #if $input_selection.gff.use == 'gff_yes'
+            -g '$input_selection.gff.gff_file'
+        #end if
+    #elif  $input_selection.input_source_selector == 'both'   
+        -n '$input_selection.nuc_file'
+        -p '$input_selection.pro_file'
+        #if $input_selection.gff.use == 'gff_yes'
+            -g '$input_selection.gff.gff_file'
+        #end if
+    #end if
+    #if str($organism) != 'None'
+        -O $organism
+    #end if
+    -o results.tsv
+    $report_common
+    #if $mutation_all == "true"
+        --mutation_all mutation_all.tsv
+    #end if
+    $gpipe
+    ]]>    </command>
+
+    <inputs>
+        <conditional name="input_selection">
+            <param name="input_source_selector" type="select" label="Input data type">
+                <option value="nuc">Nucleotide</option>
+                <option value="pro">Protein</option>
+                <option value="both">Nucleotide and Protein</option>
+            </param>
+            <when value="nuc">
+                <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/>
+            </when>
+            <when value="pro">
+                <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/>
+                <conditional name="gff">
+                    <param name="use" type="select" label="Using GFF to get genomic coordinates">
+                        <option value="gff_yes">Yes</option>
+                        <option value="gff_no" selected="true">No</option>
+                    </param>
+                    <when value="gff_yes">
+                        <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
+                    </when>
+                    <when value="gff_no">
+                    </when>
+                </conditional>
+            </when>
+            <when value="both">
+                <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/>
+                <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/>
+                <conditional name="gff">
+                    <param name="use" type="select" label="Using GFF to get genomic coordinates">
+                        <option value="gff_yes">Yes</option>
+                        <option value="gff_no" selected="true">No</option>
+                    </param>
+                    <when value="gff_yes">
+                        <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
+                    </when>
+                    <when value="gff_no">
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+                <!-- DATABASE INPUT-->
+        <param name="amrfinder_databases" label="Select a database" type="select">
+            <options from_data_table="amrfinder_databases">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
+        <param name="organism" type="select" optional="true" label="Get organism-specific results">
+            <option value="Campylobacter">Campylobacter</option>
+            <option value="Escherichia">Escherichia</option>
+            <option value="Klebsiella">Klebsiella</option>
+            <option value="Salmonella">Salmonella</option>
+            <option value="Staphylococcus">Staphylococcus</option>
+            <option value="Vibrio">Vibrio</option>
+        </param>
+        <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" />
+        <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" />
+        <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" />
+        <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" />
+        <param name="mutation_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of mutations" />
+        <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" />
+    </inputs>
+
+    <outputs>
+        <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/>
+        <data name="all_mutations" format="tabular" from_work_dir="mutation_all.tsv" label="${tool.name} on ${on_string}: All Mutations">
+            <filter>mutation_all</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test> <!-- dna input-->
+            <param name="input_source_selector" value="nuc"/>
+            <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
+            <param name="amrfinder_databases" value="2019-08-27.1" />
+            <output name="result" file="test_dna.expected" lines_diff="1"/>
+        </test>
+        <test> <!-- dna input and organism, plus gene-->
+            <param name="input_source_selector" value="nuc"/>
+            <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
+            <param name="organism" value="Escherichia" />
+            <param name="plus" value="true" />
+            <param name="amrfinder_databases" value="2019-08-27.1" />
+            <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
+        </test>
+        <test> <!-- AA input-->
+            <param name="input_source_selector" value="pro"/>
+            <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
+            <param name="amrfinder_databases" value="2019-08-27.1" />
+            <output name="result" file="test_prot.expected" lines_diff="1"/>
+        </test>
+        <test> <!-- DNA and AA input-->
+            <param name="input_source_selector" value="both"/>
+            <param name="use" value="gff_yes"/>
+            <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
+            <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
+            <param name="use" value="gff_yes"/>
+            <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
+            <param name="amrfinder_databases" value="2019-08-27.1" />
+            <output name="result" file="test_both.expected" lines_diff="1"/>
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+    This software and the accompanying database are designed to find acquired
+    antimicrobial resistance genes in bacterial protein or assembled nucleotide
+    sequences as well as known point mutations for several taxa. With
+    AMRFinderPlus we have added select members of additional classes of genes
+    such as virulence factors, biocide, heat, acid, and metal resistance genes.
+    More details: https://github.com/ncbi/amr/wiki
+                ]]>    </help>
+    <citations>
+        <citation type="doi">10.1101/550707</citation>
+    </citations>
+
+</tool>