diff callntvar.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/callntvar.xml	Mon Jun 20 20:05:57 2022 +0000
@@ -0,0 +1,52 @@
+<tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Identifies nucleotide variants</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 ntvar '${input_bam.name}' $ref_file
+
+        #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="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" ftype="bam" />
+            <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
+                    <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
+                    <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
+                    <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Nucleotide Variants
+===================
+
+Call nucleotide variants for a given BAM file and a supplied reference file.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>