diff dexseq.xml @ 5:28a2181df3b9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85

--- a/dexseq.xml	Sun Sep 27 14:06:28 2015 -0400
+++ b/dexseq.xml	Thu Oct 08 16:49:40 2015 -0400
@@ -16,25 +16,38 @@
         <regex match="Error in"
            source="both"
            level="fatal"
-           description="An undefined error occured, please check your intput carefully and contact your administrator." />
+           description="An undefined error occured, please check your input carefully and contact your administrator." />
+        <regex match="Error:"
+            source="both"
+            level="fatal"
+            description="Error in the R script." />
     </stdio>
+    <version_command>
+    <![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
+    ]]>
+    </version_command>
     <command>
     <![CDATA[
         mkdir ./html_out &&
         #import json
         Rscript $__tool_directory__/dexseq.R
             -o "$dexseq_out"
-            -p 6
+            -p \${GALAXY_SLOTS:-4}
             #set $temp_factor_names = list()
             #for $factor in $rep_factorName:
                 #set $temp_factor = list()
-                #for $level in $factor.rep_factorLevel:
-                    #set $count_files = list()
-                    #for $file in $level.countsFile:
-                        $count_files.append(str($file))
-                    #end for
-                    $temp_factor.append( {str($level.factorLevel): $count_files} )
+                #set $count_files1 = list()
+                #for $file in $factor.countFiles1:
+                    $count_files1.append(str($file))
                 #end for
+                $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
+
+                #set $count_files2 = list()
+                #for $file in $factor.countFiles2:
+                    $count_files2.append(str($file))
+                #end for
+                $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
                 $temp_factor_names.append([str($factor.factorName), $temp_factor])
             #end for
             -f '#echo json.dumps(temp_factor_names)#'
@@ -62,15 +75,21 @@
                     <valid initial="string.letters,string.digits"><add value="_" /></valid>
                 </sanitizer>
             </param>
-            <repeat name="rep_factorLevel" title="Factor level" min="2" max="2" default="2">
-                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"
-                    help="Only letters, numbers and underscores will be retained in this field">
-                    <sanitizer>
-                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
-                    </sanitizer>
-                </param>
-                <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
-            </repeat>
+            <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
+                help="Only letters, numbers and underscores will be retained in this field">
+                <sanitizer>
+                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                </sanitizer>
+            </param>
+            <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
+
+            <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
+                help="Only letters, numbers and underscores will be retained in this field">
+                <sanitizer>
+                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                </sanitizer>
+            </param>
+            <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
         </repeat>
         <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
             label="Visualise the analysis results?"
@@ -85,28 +104,20 @@
     </outputs>
     <tests>
         <test>
-            <param name="gtf" value="dexseq.gtf" ftype="bed"/>
+            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
             <repeat name="rep_factorName">
                 <param name="factorName" value="condition"/>
-                <repeat name="rep_factorLevel">
-                    <param name="factorLevel" value="knockdown"/>
-                    <param name="countsFile" value="treated1fb.txt,treated2fb.txt,treated3fb.txt"/>
-                </repeat>
-                <repeat name="rep_factorLevel">
-                    <param name="factorLevel" value="control"/>
-                    <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,untreated3fb.txt"/>
-                </repeat>
+                <param name="factorLevel1" value="knockdown"/>
+                <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
+                <param name="factorLevel2" value="control"/>
+                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
             </repeat>
             <repeat name="rep_factorName">
                 <param name="factorName" value="libtype"/>
-                <repeat name="rep_factorLevel">
-                    <param name="factorLevel" value="singleend"/>
-                    <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt"/>
-                </repeat>
-                <repeat name="rep_factorLevel">
-                    <param name="factorLevel" value="pairedend"/>
-                    <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/>
-                </repeat>
+                <param name="factorLevel1" value="singleend"/>
+                <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
+                <param name="factorLevel2" value="pairedend"/>
+                <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
             </repeat>
             <param name="report" value="False"/>
             <param name="fdr_cutoff" value="0.05"/>
@@ -124,7 +135,7 @@
 
 **Inputs**
 
-DEXSeq_ takes count tables that generated from the dexseq_count as input. Count tables must be generated for each sample individually.
+DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
 factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might
 influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.