Mercurial > repos > iuc > edger

diff edger.xml @ 2:a1634a9c2ee1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
author iuc
date Thu, 19 Apr 2018 17:26:38 -0400
parents 2a16413ec60d
children d79ed3ec25fe
line wrap: on
line diff
--- a/edger.xml	Tue Jan 30 04:07:08 2018 -0500
+++ b/edger.xml	Thu Apr 19 17:26:38 2018 -0400
@@ -1,10 +1,11 @@
-<tool id="edger" name="edgeR" version="3.20.7.0">
+<tool id="edger" name="edgeR" version="3.20.7.1">
     <description>
         Perform differential expression of count data
     </description>
 
     <requirements>
         <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
+        <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.4.30">r-statmod</requirement>
@@ -13,7 +14,7 @@
     </requirements>
 
     <version_command><![CDATA[
-echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$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: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$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: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
 
     <command detect_errors="exit_code"><![CDATA[
@@ -94,6 +95,10 @@
 
 &&
 cp '$outReport.files_path'/*.tsv output_dir/
+
+#if $out.rscript:
+    && cp '$__tool_directory__/edger.R' '$rscript'
+#end if
     ]]></command>
 
     <inputs>
@@ -222,6 +227,7 @@
                 label="Output Normalised Counts Table?"
                 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
             </param>
+            <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
             <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
                 label="Output RData file?"
                 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
@@ -259,6 +265,9 @@
         <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
         </collection>
+        <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
+            <filter>out['rscript']</filter>
+        </data>
     </outputs>
 
     <tests>
@@ -278,8 +287,18 @@
             </repeat>
             <param name="normalisationOption" value="TMM" />
             <output_collection name="outTables" count="2">
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" />
-                <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4582" />
+                   </assert_contents>
+               </element>
+                <element name="edgeR_WT-Mut" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*-0.4582" />
+                   </assert_contents>
+               </element>
             </output_collection>
             <output name="outReport" >
                 <assert_contents>
@@ -305,12 +324,18 @@
             </repeat>
             <param name="normalisationOption" value="TMM" />
             <output_collection name="outTables" count="1">
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_anno.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*Abca4.*0.4582" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
-        <!-- Ensure RData file can be output -->
+        <!-- Ensure RScript and RData file can be output -->
         <test>
             <param name="format" value="matrix" />
+            <param name="rscript" value="True"/>
             <param name="rdaOption" value="true" />
             <param name="counts" value="matrix.txt" />
             <repeat name="rep_factor">
@@ -326,6 +351,7 @@
                     <has_text text="RData" />
                 </assert_contents>
             </output>
+            <output name="rscript" value="out_rscript.txt"/>
         </test>
         <!-- Ensure secondary factors work -->
         <test>
@@ -344,7 +370,12 @@
             </repeat>
             <param name="normalisationOption" value="TMM" />
             <output_collection name="outTables" count="1" >
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4584" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
         <!-- Ensure factors file input works -->
@@ -358,7 +389,12 @@
             </repeat>
             <param name="normalisationOption" value="TMM" />
             <output_collection name="outTables" count="1">
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4584" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
         <!-- Ensure normalised counts file output works-->
@@ -375,8 +411,18 @@
             </repeat>
             <param name="normalisationOption" value="TMM" />
             <output_collection name="outTables" count="2">
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" />
-                <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4582" />
+                   </assert_contents>
+               </element>
+                <element name="edgeR_normcounts" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
+                        <has_text_matching expression="11304.*15.7535" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
         <!-- Ensure likelihood ratio option works -->
@@ -438,9 +484,24 @@
             </repeat>
             <param name="normCounts" value="true" />
             <output_collection name="outTables" count="3">
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact_anno.tsv" />
-                <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut_2fact_anno.tsv" />
-                <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts_anno.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*Abca4.*0.4584" />
+                   </assert_contents>
+               </element>
+                <element name="edgeR_WT-Mut" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*Abca4.*-0.4584" />
+                   </assert_contents>
+               </element>
+                <element name="edgeR_normcounts" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
+                        <has_text_matching expression="11304.*Abca4.*15.7535" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
         <!-- Ensure filtering on CPM in Mnimum Samples works -->
@@ -469,7 +530,13 @@
                 </assert_contents>
             </output>
             <output_collection name="outTables" count="1" >
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4568" />
+                        <not_has_text text="-0.0682" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
         <!-- Ensure filtering on Count in Minmum Samples works -->
@@ -497,7 +564,14 @@
                 </assert_contents>
             </output>
             <output_collection name="outTables" count="1" >
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4568" />
+                        <not_has_text text="-0.0682" />
+                   </assert_contents>
+               </element>
+
             </output_collection>
         </test>
         <!-- Ensure filtering on Total Count works -->
@@ -527,7 +601,13 @@
                 </assert_contents>
             </output>
             <output_collection name="outTables" count="1" >
-                <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
+                <element name="edgeR_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*0.4568" />
+                        <not_has_text text="-0.0682" />
+                   </assert_contents>
+               </element>
             </output_collection>
         </test>
     </tests>
@@ -716,6 +796,7 @@
 Optionally, under **Output Options** you can choose to output
 
     * a normalised counts table
+    * the R script used by this tool
     * an RData file
 
 -----