Mercurial > repos > bgruening > text_processing

changeset 18:1e974b82380d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
author bgruening
date Tue, 27 Feb 2018 17:10:53 -0500
parents f2918761eaf3
children bed2226b90f7
files awk.xml grep.xml recurring_lines.xml replace_text_in_column.xml replace_text_in_line.xml sed.xml sort.xml sorted_uniq.xml unfold_column.xml
diffstat 9 files changed, 26 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/awk.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/awk.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_awk_tool" name="Text reformatting" version="@BASE_VERSION@.0">
+<tool id="tp_awk_tool" name="Text reformatting" version="@BASE_VERSION@.1">
     <description>with awk</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="4.1.3">gawk</requirement>
+        <requirement type="package" version="4.2.0">gawk</requirement>
     </requirements>
     <version_command>awk --version | head -n 1</version_command>
     <command>
@@ -80,7 +80,7 @@
 - **/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. 
+- **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).
 
 
--- a/grep.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/grep.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,11 +1,11 @@
-<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.0">
+<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.1">
     <description>(grep)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="2.14">grep</requirement>
-        <requirement type="package" version="4.2.3.dev0">sed</requirement><!-- for ansi2html.sh -->
+        <requirement type="package" version="4.4">sed</requirement><!-- for ansi2html.sh -->
     </requirements>
     <version_command>grep --version | head -n 1</version_command>
     <command>
@@ -40,13 +40,13 @@
             <option value="">Match</option>
             <option value="-v">Don't Match</option>
         </param>
-        
+
         <param name="regex_type" type="select" label="Type of regex">
             <option value="-G">Basic</option>
             <option value="-P" selected="true">Perl</option>
             <option value="-E">Extended (egrep)</option>
         </param>
-        
+
         <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
             <sanitizer>
                 <valid initial="string.printable">
--- a/recurring_lines.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/recurring_lines.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -37,7 +37,7 @@
         </repeat>
     </inputs>
     <outputs>
-        <data format="text" name="outfile"/>
+        <data format="txt" name="outfile"/>
     </outputs>
     <tests>
         <test>
--- a/replace_text_in_column.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/replace_text_in_column.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.1">
+<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.2">
     <description>in a specific column</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="4.1.3">gawk</requirement>
+        <requirement type="package" version="4.2.0">gawk</requirement>
     </requirements>
     <version_command>awk --version | head -n 1</version_command>
     <command>
--- a/replace_text_in_line.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/replace_text_in_line.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,21 +1,20 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
-<tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0">
+<tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.1">
     <description>in entire line</description>
     <macros>
 	<import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="4.2.3.dev0">sed</requirement>
+        <requirement type="package" version="4.4">sed</requirement>
     </requirements>
     <version_command>sed --version | head -n 1</version_command>
     <command>
 <![CDATA[
-	sed
-            -r
-            --sandbox
-            's/$find_pattern/$replace_pattern/g'
-            '$infile'
-        > '$outfile'
+	 sed
+      -r
+      --sandbox
+      's/$find_pattern/$replace_pattern/g'
+      '$infile'
+      > '$outfile'
 ]]>
 
     </command>
--- a/sed.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/sed.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_sed_tool" name="Text transformation" version="@BASE_VERSION@.0">
+<tool id="tp_sed_tool" name="Text transformation" version="@BASE_VERSION@.1">
     <description>with sed</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="4.2.3.dev0">sed</requirement>
+        <requirement type="package" version="4.4">sed</requirement>
     </requirements>
     <version_command>sed --version | head -n 1</version_command>
     <command>
--- a/sort.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/sort.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.0">
+<tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.1">
     <description>data in ascending or descending order</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.2.3.dev0">sed</requirement>
+        <requirement type="package" version="4.4">sed</requirement>
     </expand>
     <version_command>sort --version | head -n 1</version_command>
     <command>
--- a/sorted_uniq.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/sorted_uniq.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_uniq_tool" name="Unique lines" version="@BASE_VERSION@.0">
+<tool id="tp_uniq_tool" name="Unique lines" version="@BASE_VERSION@.1">
     <description>assuming sorted input file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.2.3.dev0">sed</requirement>
+        <requirement type="package" version="4.4">sed</requirement>
     </expand>
     <version_command>uniq --version | head -n 1</version_command>
     <command>
--- a/unfold_column.xml	Tue Feb 20 09:11:35 2018 -0500
+++ b/unfold_column.xml	Tue Feb 27 17:10:53 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="tp_unfold_column_tool" name="Unfold" version="@BASE_VERSION@.0">
+<tool id="tp_unfold_column_tool" name="Unfold" version="@BASE_VERSION@.1">
     <description>columns from a table</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.7.12">python</requirement>
+        <requirement type="package" version="2.7.13">python</requirement>
     </requirements>
     <command>
 <![CDATA[