diff blockclust.xml @ 5:49b72f1013b3 draft

Uploaded

--- a/blockclust.xml	Mon Oct 21 12:34:11 2013 -0400
+++ b/blockclust.xml	Tue Oct 22 10:15:09 2013 -0400
@@ -2,6 +2,10 @@
     <description>Non-coding RNA clustering from deep sequencing read profiles</description>
     <requirements>
         <requirement type="package" version="1.0">blockclust</requirement>
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+        <requirement type="package" version="0.1.19 ">samtools</requirement>
+        <requirement type="R-module">ggplot2</requirement>
+        <requirement type="R-module">ape</requirement>
     </requirements>
     <!--<version_command> -version</version_command>-->
     <command>
@@ -61,8 +65,8 @@
                 </param>
             </when>
             <when value="post">
+                <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
                 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
-                <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
                 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
             </when>
         </conditional>
@@ -72,10 +76,10 @@
         <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
             <filter> mode["operation"]=="pre"</filter>
         </data>
-        <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
+        <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
             <filter> mode["operation"]=="clust"</filter>
         </data>
-        <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
+        <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
             <filter> mode["operation"]=="clust"</filter>
         </data>
         <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">