diff aacoverage.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/aacoverage.xml	Mon Jun 20 20:05:57 2022 +0000
@@ -0,0 +1,50 @@
+<tool id="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Builds an aa census and returns its coverage</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 aacoverage '${input_bam.name}' $ref_file $input_genes -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="input_genes" type="data" format="bed" optional="false" label="Gene 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="input_genes" ftype="bed" value="hxb2_pol.bed" />
+            <output name="output" >
+                <assert_contents>
+                    <has_text text="frame: 0" />
+                    <has_text text="1,0" />
+                    <has_text text="948,1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Amino Acid Coverage
+===================
+
+Builds an amino acid census and returns its coverage.
+
+**Output**
+
+A file with one entry per line with the AA position and the coverage at the position.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>