diff callcodonvar.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/callcodonvar.xml	Mon Jun 20 20:05:57 2022 +0000
@@ -0,0 +1,63 @@
+<tool id="callcodonvar" name="Codon Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+
+        cat $input_genes &&
+
+        ln -s $input_bam '${input_bam.name}' &&
+        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
+
+        quasitools call codonvar '${input_bam.name}' $ref_file $offset $input_genes
+
+		#if $var_file:
+			$var_file 
+		#end if
+
+        #if $error_rate:
+            -e $error_rate
+        #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="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
+        <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
+		<param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021." />
+		<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." />
+    </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="offset" value="1269"/>
+            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text text="#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count" />
+                    <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Codon Variants
+==============
+
+Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
+codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
+a synonymous or non-synonymous mutation.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>