# HG changeset patch
# User bgruening
# Date 1494090545 14400
# Node ID 60edf2f8c28fb84c390571de34b38946f0c82a4c
# Parent  20344ce0c81194c2fbeddbbdce10cf0f9f00ab22
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'

diff -r 20344ce0c811 -r 60edf2f8c28f awk.xml
--- a/awk.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/awk.xml	Sat May 06 13:09:05 2017 -0400
@@ -59,7 +59,7 @@
 
 **Further reading**
 
-- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html)
+- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1/index.html)
 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html)
 
 -----
@@ -118,4 +118,5 @@
 @REFERENCES@
 ]]>
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f cat.xml
--- a/cat.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/cat.xml	Sat May 06 13:09:05 2017 -0400
@@ -87,5 +87,7 @@
     chr2  100000015  200000999  Q  0  +
 
 @REFERENCES@
-]]></help>
+]]>
+    </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f cut.xml
--- a/cut.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/cut.xml	Sat May 06 13:09:05 2017 -0400
@@ -106,6 +106,10 @@
                                             <filter type="metadata_value" ref="input" name="endCol" column="3" />
                                         </option>
                                     </action>
+                                </when>
+                            </conditional>
+                        </when>
+                        </conditional>        
                         <conditional name="output">
                             <when datatype_isinstance="interval">
                                 <action type="metadata" name="chromCol">
@@ -172,15 +176,11 @@
                                         <filter type="metadata_value" ref="input" name="strandCol" column="1" />
                                     </option>
                                 </action>
-                          </when>
+                            </when>
                         </conditional>
-                      </when>
-                    </conditional>
-                  </when>
+                    </when>
                 </conditional>
-              </when>
-            </conditional>
-          </actions>
+            </actions>
         </data>
     </outputs>
     <tests>
@@ -256,4 +256,5 @@
 @REFERENCES@
 ]]>
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f easyjoin.xml
--- a/easyjoin.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/easyjoin.xml	Sat May 06 13:09:05 2017 -0400
@@ -112,4 +112,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f find_and_replace.xml
--- a/find_and_replace.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/find_and_replace.xml	Sat May 06 13:09:05 2017 -0400
@@ -178,4 +178,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f grep.xml
--- a/grep.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/grep.xml	Sat May 06 13:09:05 2017 -0400
@@ -190,4 +190,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f head.xml
--- a/head.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/head.xml	Sat May 06 13:09:05 2017 -0400
@@ -59,4 +59,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f multijoin.xml
--- a/multijoin.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/multijoin.xml	Sat May 06 13:09:05 2017 -0400
@@ -129,4 +129,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f recurring_lines.xml
--- a/recurring_lines.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/recurring_lines.xml	Sat May 06 13:09:05 2017 -0400
@@ -75,4 +75,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f replace_text_in_column.xml
--- a/replace_text_in_column.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/replace_text_in_column.xml	Sat May 06 13:09:05 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0">
+<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.1">
     <description>in a specific column</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,8 @@
     <command>
 <![CDATA[
         awk
-            -v OFS="	"
+            -v OFS="\t"
+            -v FS="\t"
             --re-interval
             --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }'
             "$infile"
@@ -132,4 +133,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f replace_text_in_line.xml
--- a/replace_text_in_line.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/replace_text_in_line.xml	Sat May 06 13:09:05 2017 -0400
@@ -73,7 +73,7 @@
 **Examples of Replace Patterns**
 
 - **WORLD**  The word 'WORLD' will be placed whereever the find pattern was found.
-- **FOO-&-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$** (ampersand) represents the matched find pattern.
+- **FOO-&-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the beginning and '-BAR' at the end. **&** (ampersand) represents the matched find pattern.
 - **\\1**   The text which matched the first parenthesis in the Find Pattern.
 
 
@@ -129,4 +129,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f sed.xml
--- a/sed.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/sed.xml	Sat May 06 13:09:05 2017 -0400
@@ -129,4 +129,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f sort.xml
--- a/sort.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/sort.xml	Sat May 06 13:09:05 2017 -0400
@@ -173,4 +173,5 @@
 @REFERENCES@
 ]]>
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f sort_rows.xml
--- a/sort_rows.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/sort_rows.xml	Sat May 06 13:09:05 2017 -0400
@@ -34,4 +34,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f sorted_uniq.xml
--- a/sorted_uniq.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/sorted_uniq.xml	Sat May 06 13:09:05 2017 -0400
@@ -102,4 +102,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f tac.xml
--- a/tac.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/tac.xml	Sat May 06 13:09:05 2017 -0400
@@ -87,4 +87,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f tail.xml
--- a/tail.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/tail.xml	Sat May 06 13:09:05 2017 -0400
@@ -64,4 +64,5 @@
 @REFERENCES@
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f unfold_column.xml
--- a/unfold_column.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/unfold_column.xml	Sat May 06 13:09:05 2017 -0400
@@ -63,4 +63,5 @@
 @REFERENCES@
 ]]>
   </help>
+  <expand macro="citations" />
 </tool>
diff -r 20344ce0c811 -r 60edf2f8c28f unsorted_uniq.xml
--- a/unsorted_uniq.xml	Wed Nov 23 15:56:41 2016 -0500
+++ b/unsorted_uniq.xml	Sat May 06 13:09:05 2017 -0400
@@ -90,4 +90,5 @@
 @REFERENCES@
 ]]>
 </help>
+<expand macro="citations" />
 </tool>