diff egsea.xml @ 1:73281fbdf6c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0

--- a/egsea.xml	Thu Jan 25 02:23:23 2018 -0500
+++ b/egsea.xml	Thu Feb 15 02:34:59 2018 -0500
@@ -1,12 +1,14 @@
-<tool id="egsea" name="EGSEA" version="1.6.0.0">
+<tool id="egsea" name="EGSEA" version="1.6.0.1">
     <description> easy and efficient ensemble gene set testing</description>
     <requirements>
         <requirement type="package" version="1.6.0">bioconductor-egsea</requirement>
         <requirement type="package" version="1.4.4">r-optparse</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
+        <!--statmod is required for fry-->
+        <requirement type="package" version="1.4.30">r-statmod</requirement>
     </requirements>
     <version_command><![CDATA[
-echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
 ## EGSEA requires at least 2 threads
@@ -57,6 +59,7 @@
 --base_methods $base_methods
 --msigdb $msigdb.msigdb_gsets
 --keggdb $keggdb.keggdb_gsets
+--keggupdated $keggdb.kegg_updated
 --gsdb $gsdb.gsdb_gsets
 
 --display_top $advanced.display_top
@@ -186,6 +189,7 @@
                 <option value="keggsig">Signalling pathways</option>
                 <option value="keggdis">Disease pathways</option>
             </param>
+            <param name="kegg_updated" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Download KEGG pathways?" help="Select Yes if you want to download the most recent KEGG pathways, see the Help section below. Default: No"/>
         </section>
 
         <section name="gsdb" title="GeneSetDB Gene Sets" expanded="True">
@@ -259,7 +263,7 @@
     </outputs>
 
     <tests>
-         <!-- Ensure report is output -->
+        <!-- Ensure report is output -->
         <test expect_num_outputs="1">
             <param name="non_commercial_use" value="True"/>
             <param name="format" value="matrix" />
@@ -338,6 +342,40 @@
                 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/>
             </output_collection>
         </test>
+        <!-- Ensure all gene set methods work -->
+        <test expect_num_outputs="1">
+            <param name="non_commercial_use" value="True"/>
+            <param name="format" value="matrix"/>
+            <param name="counts" value="il13.counts"/>
+            <param name="genes" value="il13.genes"/>
+            <param name="ffile" value="yes"/>
+            <param name="finfo" value="il13.group_batch"/>
+            <repeat name="rep_contrast">
+                <param name="contrast" value="IL13Ant-IL13"/>
+            </repeat>
+            <param name="base_methods" value="camera,safe,gage,zscore,gsva,globaltest,ora,ssgsea,padog,plage,fry,roast"/>
+            <output_collection name="outTables" count="1">
+                <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch_all.txt"/>
+            </output_collection>
+        </test>
+        <!-- Ensure KEGG updated works -->
+        <test expect_num_outputs="1">
+            <param name="non_commercial_use" value="True"/>
+            <param name="format" value="matrix"/>
+            <param name="counts" value="il13.counts"/>
+            <param name="genes" value="il13.genes"/>
+            <param name="ffile" value="yes"/>
+            <param name="finfo" value="il13.group_batch"/>
+            <repeat name="rep_contrast">
+                <param name="contrast" value="IL13Ant-IL13"/>
+            </repeat>
+            <param name="keggdb_gsets" value="keggmet"/>
+            <param name="kegg_updated" value="True"/>
+            <output_collection name="outTables" count="2">
+                <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/>
+                <element name="ranked-kegg-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-kegg-gene-sets-IL13Ant-IL13.txt"/>
+            </output_collection>
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -528,7 +566,7 @@
 
 **KEGG Pathways**
 
-Obtained by EGSEAdata from the GAGE_ Bioconductor package using the gage function kegg.gsets(). The Pathview_ Bioconductor package is used to visualize the expression data mapped onto the KEGG pathway graphs. Pathview has a GPLv3 licence which means users are required to formally cite the original `Pathview paper`_ (not just mention it) in publications or products. GAGE/Pathview divide the KEGG pathways into 3 categories: Signaling, Metabolism and Disease, listed in this file at the `Pathview website here`_.
+Obtained by EGSEAdata from the GAGE_ Bioconductor package using the gage function kegg.gsets(). The Pathview_ Bioconductor package is used to visualize the expression data mapped onto the KEGG pathway graphs. Pathview has a GPLv3 licence which means users are required to formally cite the original `Pathview paper`_ (not just mention it) in publications or products. GAGE/Pathview divide the KEGG pathways into 3 categories: Signaling, Metabolism and Disease, listed in this file at the `Pathview website here`_. You can choose if you want to download the most recent KEGG pathways by selecting the ``Download KEGG pathways`` option in the tool form above. Note that downloading the most recent pathways may affect reproducibility as you can't choose what versions of pathways to use.
 
 **Signaling**