changeset 0:2e05d9335bae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_cov_stats.xml	Tue Jun 11 12:28:13 2024 +0000
@@ -0,0 +1,40 @@
+<tool id="get_cov_stats" name="get statistics from bam file" version="1">
+  <description>
+    From bam file, get some statistics
+  </description>
+  <requirements>
+    <requirement type="package" version="3.6.0">r</requirement>
+    <requirement type="package" version="1.14">samtools</requirement>
+    <requirement type="package" version="3.7.12">python</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+    python '$__tool_directory__/get_cov_stats.py' 
+      -bam "$bamfile" 
+      #if $typeofreads.p_or_s == "paired":
+        -p
+      #end if
+      > "$output"
+  ]]></command>
+  <inputs>
+    <param name="bamfile" type="data" format="bam" label="Bam file" help="Bam file of an aligment"/>
+    <conditional name="typeofreads">
+      <param name="p_or_s" type="select" label="Read option">
+        <option value="single" selected="True">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <help>
+  <![CDATA[
+
+Homemade script to get some statistics about and bam file.
+
+  ]]>
+  </help>
+</tool>