Mercurial > repos > iuc > edger

diff edger.xml @ 3:d79ed3ec25fe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
author iuc
date Sun, 06 May 2018 13:38:41 -0400
parents a1634a9c2ee1
children 4730985c816f
line wrap: on
line diff
--- a/edger.xml	Thu Apr 19 17:26:38 2018 -0400
+++ b/edger.xml	Sun May 06 13:38:41 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="edger" name="edgeR" version="3.20.7.1">
+<tool id="edger" name="edgeR" version="3.20.7.2">
     <description>
         Perform differential expression of count data
     </description>
@@ -120,12 +120,12 @@
                     </param>
                     <repeat name="rep_group" title="Group" min="2" default="2">
                         <param name="groupName" type="text" label="Name"
-                        help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
+                        help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
                         <sanitizer>
                             <valid initial="string.letters,string.digits"><add value="_" /></valid>
                         </sanitizer>
                         </param>
-                        <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
+                        <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
                     </repeat>
                 </repeat>
             </when>
@@ -683,19 +683,19 @@
 **Gene Annotations:**
 Optional input for gene annotations, this can contain more
 information about the genes than just an ID number. The annotations will
-be available in the differential expression results table and the optional normalised counts table.
+be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
 
 Example:
 
     ==========  ==========  ===================================================
     **GeneID**  **Symbol**  **GeneName**
     ----------  ----------  ---------------------------------------------------
-    1287        Pzp         pregnancy zone protein
-    1298        Aanat       arylalkylamine N-acetyltransferase
-    1302        Aatk        apoptosis-associated tyrosine kinase
-    1303        Abca1       ATP-binding cassette, sub-family A (ABC1), member 1
-    1304        Abca4       ATP-binding cassette, sub-family A (ABC1), member 4
-    1305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
+    11287        Pzp         pregnancy zone protein
+    11298        Aanat       arylalkylamine N-acetyltransferase
+    11302        Aatk        apoptosis-associated tyrosine kinase
+    11303        Abca1       ATP-binding cassette, sub-family A (ABC1), member 1
+    11304        Abca4       ATP-binding cassette, sub-family A (ABC1), member 4
+    11305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
     ==========  ==========  ===================================================
 
 **Contrasts of Interest:**