diff rgGSEA/rgGSEAcolumns.xml @ 4:89e89b70a867 draft default tip

Uploaded

--- a/rgGSEA/rgGSEAcolumns.xml	Sun Jun 09 02:06:52 2013 -0400
+++ b/rgGSEA/rgGSEAcolumns.xml	Sun Jun 09 23:09:34 2013 -0400
@@ -18,9 +18,12 @@
 #if $gmtSource.refgmtSource == "history" or $gmtSource.refgmtSource == "both":
 --history_gmt "${gmtSource.ownGMT}" --history_gmt_name "${gmtSource.ownGMT.name}"
 #end if
-#if $checkchip.convertchip=="yes"
- --chip "${checkchip.use_chip.fields.path}"
-#end if  
+#if $chipSource.refchipSource=="builtin"
+ --chip "${chipSource.builtinChip.fields.path}"
+#end if
+#if $chipSource.refchipSource=="history"
+ --chip "${chipSource.ownChip}"
+#end if
 </command>
   <inputs>
     <param name="input1"  type="data" format="tabular" label="Select a tab delimited file with a probe id, adjusted p value and a signed weight (eg t-test statistic) on each row"
@@ -55,21 +58,28 @@
         <option value="Yes">Yes</option>
         <option value="No" selected="true">No</option>
     </param>
-    <conditional name="checkchip" >
-        <param name="convertchip" type="select" label="Translate the rank file IDs (first column) using a GSEA 'chip' lookup table">
-        <option value="yes">Use a GSEA 'chip' file</option>
+    <conditional name="chipSource" >
+        <param name="refchipSource" type="select" label="Translate the rank file IDs (first column) using a GSEA 'chip' lookup table">
+        <option value="builtin">Use a builtin GSEA 'chip' file</option>
+        <option value="history">Use one of the GSEA 'chip' files in my history</option>
         <option value="no" selected="true">IDs are already gene symbols - no translation needed  </option>
         </param>
         <when value="no">
         </when>
-        <when value="yes">
-           <param name="use_chip" type="select" label="Select a GSEA 'chip' for the probe ids or symbols in the ranks file">
+        <when value="builtin">
+           <param name="builtinChip" type="select" label="Select a GSEA 'chip' to map each probe id in the input file to a gene symbol">
               <options from_data_table="gseaChip_3.1">
               <filter type="sort_by" column="2" />
               <validator type="no_options" message="No chip tables are available - please see the Galaxy GSEA tool documentation for instructions on installing them" />
               </options>
            </param>
         </when>
+      <when value="history">
+        <param name="ownChip" type="data" format="gseachip" label="Select an existing gseachip filefrom your history. Probe_id matching ids in your input file and a gene_symbol must be the first 2 tabular columns. Header row required."
+           help='see docs at http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CHIP:_Chip_file_format_.28.2A.chip.29'>
+            <validator type="no_options" message="Need a gseachip datatype - tabular file, probe_id gene_symbol as first 2 columns. Header row required. Convert datatypes (pencil icon) of existing history tabular files if necessary"/>
+        </param>
+      </when>
     </conditional>
     <conditional name="gmtSource">
       <param name="refgmtSource" type="select" label="Use a gene set (.gmt) from your history or use a built-in (MSigDB etc) gene set">
@@ -89,11 +99,11 @@
         <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
       </when>
       <when value="both">
-        <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
+        <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
         <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
           <options from_data_table="gseaGMT_3.1">
             <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
+            <validator type="no_options" message="No GMT v3.1 files are available - please install them and make sure they match [tool-data]/gseaGMT_3.1.loc, editing as needed"/>
           </options>
         </param>
        </when>
@@ -107,8 +117,33 @@
     <data format="tabular" name="outtab_neg" label="${title}_neg_allsets.xls">
     <filter>makeTab=="Yes"</filter>
     </data>
-
   </outputs>
+  <tests>
+  <test>
+      <param name="input1" value="gsea_test_DGE.xls"/>
+      <param name="ownGMT" value="gsea_test_DGE.xls"/>
+      <param name="adjpvalcol" value="5"/>
+      <param name="signcol" value="2"/>
+      <param name="idcol" value="1"/>
+      <param name="plotTop" value="2"/>
+      <param name="makeTab" value="No"/>
+      <param name="refchipSource" value="no"/>
+      <param name="refgmtSource" value="history"/>
+      <param name="html_file" value="gseatestout.html">
+         <assert_contents>
+              <has_text text="GSEA Report for Dataset" />
+              <has_text text="enrichment results in html"/>
+         </assert_contents>
+      </param>
+      <param name="setMax" value="500"/>
+      <param name="setMin" value="15"/>
+      <param name="nPerm" value="100"/>
+      <param name="output_dir" value="gseatestout"/>
+      <param name="mode" value="Max_probe"/>
+      <param name="title" value="GSEA test"/>
+      <param name="builtin_gmt" value="gseatestdata.gmt"/>
+  </test>
+  </tests>
 <help>
 **What it does**