diff callaavar.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/callaavar.xml	Mon Jun 20 20:05:57 2022 +0000
@@ -0,0 +1,76 @@
+<tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Identifies amino acid mutations</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 call aavar '${input_bam.name}' $ref_file $input_genes 
+		
+		#if $var_file:
+			$var_file 
+		#end if
+
+        #if $mutation_db:
+        	$mutation_db
+        #end if
+
+		#if $min_freq:
+			-f $min_freq 
+		#end if
+
+		#if $error_rate:
+            -e $error_rate
+        #end if
+
+        -o output.vcf
+
+    ]]></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="input_genes" type="data" format="bed" optional="false" label="Gene file" />
+		<param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
+        <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
+        <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="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="output" from_work_dir="output.vcf" />
+    </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="min_freq" value="0.01" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text_matching expression="#CHROM"/>
+                    <has_text_matching expression="0.0779" />
+                    <has_text_matching expression="0.0103;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0163;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0148;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0234;CAT=.;SRVL=." />
+                    <has_text_matching expression="0.0159;CAT=.;SRVL=." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Amino Acid Variants
+===================
+
+Identifies amino acid mutations for a BAM file.
+
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>