diff macs2_randsample.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

--- a/macs2_randsample.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_randsample.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -7,48 +7,62 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command>
+        <![CDATA[
         macs2 randsample
-            -t "${ infile }"
-            -o "${ outfile }"
+            -t '${ infile }'
+            -o '${ outfile }'
+            --seed '${ seed }'
 
-        --format '${ infile.extension.upper() }'
+            --format '${ infile.extension.upper() }'
 
-        @tag_size@
+            @tag_size@
+
         #if $method_options.method_options_selector == 'percentage':
-            --percentage "${ method_options.percentage }"
+            --percentage '${ method_options.percentage }'
         #else:
-            --number "${ method_options.number }"
+            --number '${ method_options.number }'
         #end if
+        ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
         <expand macro="tag_size" />
-
         <conditional name="method_options">
             <param name="method_options_selector" type="select" label="Select action to be performed">
                 <option value="percentage" selected="true">Percentage</option>
                 <option value="number">Number</option>
             </param>
             <when value="percentage">
-                    <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
+                    <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/>
             </when>
             <when value="number">
                     <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
             </when>
         </conditional>
+        <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/>
     </inputs>
     <outputs>
         <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
-        <!-- No test, due to the randomness -->
+        <test>
+            <param name="infile" value="ChIP_200K.bed" ftype="bed" />
+            <param name="method_options_selector" value="percentage" />
+            <param name="percentage" value="80.0" />
+            <param name="seed" value="1" />
+            <output name="outfile" file="bdgrandsample_output.bed"/>
+        </test> 
     </tests>
     <help>
+        <![CDATA[
 **What it does**
 
-randsample tool from macs2
+This is **randsample** utility from the MACS2_ Package. It randomly samples reads by number or percentage from an input file.
+
+.. _MACS2: https://github.com/taoliu/MACS
 
 @citation@
+]]>
   </help>
   <expand macro="citations" />
 </tool>