diff deseq2.xml @ 20:bbea9c694b34 draft

Uploaded

--- a/deseq2.xml	Mon Sep 30 12:28:02 2013 -0400
+++ b/deseq2.xml	Wed Feb 19 06:11:20 2014 -0500
@@ -8,7 +8,7 @@
         <!--<requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>-->
     </requirements>
     <command interpreter="Rscript">
-        #import simplejson
+        #import json
         deseq2.R
             -o "$deseq_out"
             --outfilefiltered "$deseq_out_filtered"
@@ -16,7 +16,7 @@
             #if $pdf:
                 -p "$plots" 
             #end if
-            
+
             -i "$input_matrix"
 
             #set $temp_factor_name = list()
@@ -31,7 +31,7 @@
             #end for
 
                 ##-m "#echo ' '.join( $temp_factor_list )#"
-                -m '#echo simplejson.dumps(temp_factor_name)#'
+                -m '#echo json.dumps(temp_factor_name)#'
             ##--organism "$organism"
             ##-t "$fittype"
             -c $countthreshold
@@ -53,15 +53,15 @@
     <inputs>
         <param format="tabular" name="input_matrix" type="data" label="Countmatrix" help="You can create a count matrix with the tool 
             'Count reads in features with htseq-count'"/>
-        
+
         <repeat name="rep_factorName" title="Factor/Condition" min="1">
-            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" help=""/>
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" help="" />
             <repeat name="rep_factorLevel" title="Factor level" min="1">
-                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level" help=""/>
+                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level" help="" />
 
                 <param name="factorIndex" label="Select columns that are associated with this factor level" type="data_column" data_ref="input_matrix"
                     numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
-                    <validator type="no_options" message="Please select at least one column."/>
+                    <validator type="no_options" message="Please select at least one column." />
                 </param>
             </repeat>
         </repeat>
@@ -90,24 +90,25 @@
             <option value="fly">fly</option>
             <option value="other">other</option>
         </param-->
-        <param name="countthreshold" size="10" type="float" value="10" label="Filter out features with mean normalized counts lower than this value"/>
+        <param name="countthreshold" size="10" type="float" value="10.0" label="Filter out features with mean normalized counts lower than this value"/>
         <param name="fittype" type="select" label="Type of fitting of dispersions to the mean intensity">
             <option value="parametric">parametric</option>
             <option value="local">local</option>
             <option value="mean">mean</option>
-        </param> 
-        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" label="Visualising the analysis results"
-            help="output an additional PDF files" />            
+        </param>
+        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 
+            label="Visualising the analysis results"
+            help="output an additional PDF files" />
     </inputs>
 
     <outputs>
-        <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"/>
-        <data format="tabular" name="deseq_out_filtered" label="Independent filtering result file on ${on_string}"/>
+        <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}" />
+        <data format="tabular" name="deseq_out_filtered" label="Independent filtering result file on ${on_string}" />
         <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
             <filter>pdf == True</filter>
         </data>
     </outputs>
-    <code file="matrix_helper.py" />
+    <code file="deseq_helper.py" />
 
     <help>
 
@@ -147,7 +148,7 @@
 
 DESeq2_ Authors: Michael Love (MPIMG Berlin), Simon Anders, Wolfgang Huber (EMBL Heidelberg)
 
-If _DESeq2_ is used to obtain results for scientific publications it
+If DESeq2_ is used to obtain results for scientific publications it
 should be cited as [1]_. A paper describing DESeq2_ is in preparation.