diff drmutations.xml @ 0:1f1214983a1c draft default tip

planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/drmutations.xml	Mon Jun 20 20:05:57 2022 +0000
@@ -0,0 +1,88 @@
+<tool id="drmutations" name="Drug Resistance Mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools drmutations '${input_bam.name}' $ref_file $var_file $input_genes
+
+        #if $mutation_db:
+          $mutation_db
+        #end if
+
+        #if $min_freq:
+            -f $min_freq
+        #end if
+
+        #if $reporting_thres:
+            -t $reporting_thres
+        #end if
+
+        -o output.csv
+
+    ]]></command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
+        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
+        <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
+        <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
+        <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" />
+        <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
+        <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1"
+            help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" from_work_dir="output.csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="align.bam" />
+            <param name="ref_file" value="hxb2_pol.fas" />
+             <param name="var_file" value="nt_variants.vcf" />
+            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
+            <param name="mutation_db" value="mutation_db.tsv" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
+                    <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Drug Resistance Mutations
+=========================
+
+Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
+
+------
+Inputs
+------
+
+1. A BAM file.
+2. A reference FASTA file.
+3. A variants (.vcf) file.
+4. A genes (.bed) file.
+5. A mutation database (.tsv) file.
+
+----------
+Parameters
+----------
+1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
+2. The reporting threshold a mutation must pass to be included in the report.
+
+-------
+Outputs
+-------
+
+A CSV file containing the drug resistant mutations found.
+
+    ]]></help>
+	<expand macro="citations" />
+</tool>