diff covstats.xml @ 0:f0f2795de2c7 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covstats.xml	Tue Dec 19 04:54:04 2017 -0500
@@ -0,0 +1,57 @@
+<tool id="mimodd_covstats" name="MiModD Coverage Statistics" 
+version="@MIMODD_WRAPPER_VERSION@">
+    <description>
+    calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+    mimodd covstats '$ifile' --ofile '$ofile'
+    ]]></command>
+
+    <inputs>
+        <param name="ifile" type="data" format="bcf" label="BCF input file" 
+        help="Use the Variant Calling tool to generate input for this tool."/>
+    </inputs>
+    <outputs>
+        <data name="ofile" format="tabular" 
+        label="Coverage Statistics for ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="ifile" value="a.bcf" />
+            <output name="ofile" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="3" />
+                    <has_line_matching expression="^chrI&#009;.+" />
+                    <has_line_matching expression="^chrII&#009;.+" />
+                    <has_line_matching expression="^chrIII&#009;.+" />
+                    <has_line_matching expression="^chrIV&#009;.+" />
+                    <has_line_matching expression="^chrV&#009;.+" />
+                    <has_line_matching expression="^chrX&#009;.+" />
+                    <has_line_matching expression="^MtDNA&#009;.+" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+.. class:: infomark
+
+   **What it does**
+
+The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
+
+.. class:: warningmark
+
+   The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites.
+
+@HELP_FOOTER@
+    ]]></help>
+    <expand macro="citations" />
+</tool>