# HG changeset patch
# User marpiech
# Date 1485962957 18000
# Node ID 4cdaf6059e84fc708b54176760417ba79fea45e4
# Parent  2fee8da6aabbb1ca47edd4c1f3fb86ea5de44446
planemo upload

diff -r 2fee8da6aabb -r 4cdaf6059e84 countmatrixforedger.xml
--- a/countmatrixforedger.xml	Fri Dec 23 06:42:19 2016 -0500
+++ b/countmatrixforedger.xml	Wed Feb 01 10:29:17 2017 -0500
@@ -20,9 +20,9 @@
     </command>
     <inputs>
         <repeat name="sample" title="">
-            <param name="sample_data" type="data" format="data" label="" help="" />
-            <param name="sample_name" type="text" label="" help="" />
-            <param name="sample_group" type="text" label="" help="" />
+            <param name="sample_data" type="data" format="data" label="Output matrix from EDGE-pro (out_rpkm)" />
+            <param name="sample_name" type="text" label="" help="Sample name" />
+            <param name="sample_group" type="text" label="" help="Sample group name- it has to be the same string for each sample of this group" />
         </repeat>
     </inputs>
     <outputs>
@@ -54,6 +54,7 @@
     </tests>
     <help>
         <![CDATA[ 
+
      ]]>
     </help>
         <citations>
diff -r 2fee8da6aabb -r 4cdaf6059e84 plotheatmap.xml
--- a/plotheatmap.xml	Fri Dec 23 06:42:19 2016 -0500
+++ b/plotheatmap.xml	Wed Feb 01 10:29:17 2017 -0500
@@ -1,24 +1,32 @@
 <tool id="plotheatmap" name="plotHeatmap" version="1.0">
     <description>Plot heatmap</description>
+    <requirements>
+        <requirement type="package" version="3.0.1">r-gplots</requirement>
+    </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command>
         <![CDATA[ 
-            $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $main.log_fc $main.log_cpm $main.pvalue $main.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log
+            $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $filter.log_fc $filter.log_cpm $filter.pvalue $filter.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log
 
         ]]>
     </command>
     <inputs>
         <section name="main" title="Main parameters" expanded="True">
-            <param name="count_matrix" type="data" format="data" label=""/>
-            <param name="stats_matrix" type="data" format="data" label=""/>
-            <param name="log_fc" type="float" value="0.5" label=""/>
-            <param name="log_cpm" type="float" value="0.5" label=""/>
-            <param name="pvalue" type="float" value="0.5" label=""/>
-            <param name="fdr" type="float" value="0.5" label=""/>
+            <param name="count_matrix" type="data" format="data" label="Output dataset 'count_matrix' from tool countMatrixForEdger"/>
+            <param name="stats_matrix" type="data" format="data" label="Output dataset 'output' from tool edgeR"/>
         </section>
-
+        <section name="filter" title="Filtering parameters" expanded="True">
+            <param name="log_fc" type="float" value="0.5" label="A log FC threshold"/>
+            <param name="log_cpm" type="float" value="0.5" label="A log CPM threshold"/>
+            <param name="pvalue" type="float" value="0.5" label="A PValue threshold">
+                <validator type="in_range" min="0" max="1" />
+            </param>
+            <param name="fdr" type="float" value="0.5" label="A FDR threshold">
+                <validator type="in_range" min="0" max="1" />            
+            </param>
+        </section>
         <section name="heatmap" title="Heatmap parameters">
             <param name="cluster_row" type="select" label="Determines if the row dendrogram should be reordered">
                 <option value="No" >No </option>
@@ -43,14 +51,12 @@
 
 
        <section name="plotparm" title="Plot parameters">
-            <param name="col_marg" type="float" value="7" label="Margins or column names"/>
-            <param name="row_marg" type="float" value="8" label="Margins or row names"/>
-            <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches" />
-            <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches" />
+            <param name="col_marg" type="float" value="7" label="Margins for column names"/>
+            <param name="row_marg" type="float" value="8" label="Margins for row names"/>
+            <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches (pdf width)" />
+            <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches (pdf height)" />
         </section>
 
-
-
     </inputs>
     <outputs>
        <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
@@ -77,7 +83,19 @@
     </tests>
     <help>
         <![CDATA[ 
-
+**What it does**
+It takes a list of genes basen on set filtering criteria and draws them on heatmap.
+**Example**
+The following filtering options:
+A log FC threshold = 0.5
+A log CPM threshold = 0.5
+A PValue threshold = 0.05
+A FDR threshold = 0.1
+mean that you select genes whose values in output table from edgeR are:
+* absolute value of logFC is greater than or equal 0.5 
+* logCPM is greater than or equal 0.5
+* PValue is less than or equal to 0.05
+* FDR is less than or equal to 0.1
      ]]>
     </help>
     <citations>