changeset 15:74aae7d6cb09 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

--- a/awk.xml	Sat May 06 13:09:30 2017 -0400
+++ b/awk.xml	Wed Jul 12 14:06:47 2017 -0400
@@ -80,14 +80,17 @@
 - **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
 - **$7 ~ /A{4}U/**  will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
 - **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
+- **BEGIN** will be executed once only, before the first input record is read. 
 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).
 
 
+
 **Action Examples**
 
 - **{ print }** or **{ print $0 }**   will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'.
 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
 - **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length).
+- **{ FS = "," }** can be used to change the field separator (delimeter) for parsing the input file.
 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line.
 
 

--- a/easyjoin.xml	Sat May 06 13:09:30 2017 -0400
+++ b/easyjoin.xml	Wed Jul 12 14:06:47 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="tp_easyjoin_tool" name="Join" version="@BASE_VERSION@.0">
+<tool id="tp_easyjoin_tool" name="Join" version="@BASE_VERSION@.1">
     <description>two files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="5.22.0.1">perl</requirement>
     </expand>
     <version_command>join --version | head -n 1</version_command>
     <command>

--- a/find_and_replace.xml	Sat May 06 13:09:30 2017 -0400
+++ b/find_and_replace.xml	Wed Jul 12 14:06:47 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="tp_find_and_replace" name="Replace" version="@BASE_VERSION@.0">
+<tool id="tp_find_and_replace" name="Replace" version="@BASE_VERSION@.1">
     <description>parts of text</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="5.22.0.1">perl</requirement>
     </requirements>
     <command>
 <![CDATA[

--- a/multijoin.xml	Sat May 06 13:09:30 2017 -0400
+++ b/multijoin.xml	Wed Jul 12 14:06:47 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="tp_multijoin_tool" name="Multi-Join" version="@BASE_VERSION@.0">
+<tool id="tp_multijoin_tool" name="Multi-Join" version="@BASE_VERSION@.1">
     <description>(combine multiple files)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="5.22.0.1">perl</requirement>
     </requirements>
     <command>
 <![CDATA[
@@ -44,7 +44,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="outfile" format_source="first_file" metadata_source="first_file" />
+        <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>

--- a/tac.xml	Sat May 06 13:09:30 2017 -0400
+++ b/tac.xml	Wed Jul 12 14:06:47 2017 -0400
@@ -70,19 +70,20 @@
 
 Input file:
 
- 0 1 2 3 4 5 # 6 7 8 9
+    0 1 2 3 4 5 # 6 7 8 9
 
 
 default settings:
 
- 9 8 7 6 # 5 4 3 2 1 0
+    9 8 7 6 # 5 4 3 2 1 0
 
 with option -s 5:
- # 6 7 8 9 0 1 2 3 4 5
+
+    # 6 7 8 9 0 1 2 3 4 5
 
 with option -b and -s 5:
 
- 5 # 6 7 8 9 0 1 2 3 4
+    5 # 6 7 8 9 0 1 2 3 4
 
 @REFERENCES@
 ]]>