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changeset 12:062ed2bb4f2e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f8896018f5b980a456c4ceaffe0ed457dc80b5a8
author bgruening
date Thu, 02 Jun 2016 08:58:39 -0400
parents e6d48dc4e6ba
children 3c685c4106b3
files awk.xml grep.xml macros.xml multijoin multijoin.xml replace_text_in_column.xml replace_text_in_line.xml sed.xml test-data/grep_results2.html text_processing.tar.bz2 tool_dependencies.xml
diffstat 11 files changed, 9 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- a/awk.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/awk.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+        <requirement type="package" version="4.1.3">gawk</requirement>
     </expand>
     <version_command>awk --version | head -n 1</version_command>
     <command>
--- a/grep.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/grep.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.14">gnu_grep</requirement>
+        <requirement type="package" version="2.14">grep</requirement>
     </expand>
     <version_command>grep --version | head -n 1</version_command>
     <command>
--- a/macros.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/macros.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -1,11 +1,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="8.22">gnu_coreutils</requirement>
+            <requirement type="package" version="8.25">coreutils</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@BASE_VERSION@">1.0</token>
+    <token name="@BASE_VERSION@">1.1</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
--- a/multijoin	Fri Mar 18 15:18:21 2016 -0400
+++ b/multijoin	Thu Jun 02 08:58:39 2016 -0400
@@ -5,7 +5,6 @@
 use Data::Dumper;
 use Carp;
 use File::Basename;
-use Sort::Key::Natural qw(natsort);
 
 my $version = "0.1.1";
 my $field_sep = "\t";
@@ -68,7 +67,7 @@
 
 sub print_combined_data()
 {
-	my @keys = natsort keys %data ;
+	my @keys = sort keys %data ;
 
 	foreach my $key ( @keys ) {
 		my @outputs;
--- a/multijoin.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/multijoin.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -54,7 +54,7 @@
             <param name="key_column" value="4" />
             <param name="value_columns" value="c7,c8,c9" />
             <param name="output_header" value="True" />
-            <output name="outfile" file="multijoin_result1.txt" />
+            <output name="outfile" file="multijoin_result1.txt" lines_diff="2" />
         </test>
     </tests>
     <help>
--- a/replace_text_in_column.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/replace_text_in_column.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+        <requirement type="package" version="4.1.3">gawk</requirement>
     </expand>
     <version_command>awk --version | head -n 1</version_command>
     <command>
--- a/replace_text_in_line.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/replace_text_in_line.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
+        <requirement type="package" version="4.2.2">sed</requirement>
     </expand>
     <version_command>sed --version | head -n 1</version_command>
     <command>
--- a/sed.xml	Fri Mar 18 15:18:21 2016 -0400
+++ b/sed.xml	Thu Jun 02 08:58:39 2016 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
+        <requirement type="package" version="4.2.2">sed</requirement>
     </expand>
     <version_command>sed --version | head -n 1</version_command>
     <command>
--- a/test-data/grep_results2.html	Fri Mar 18 15:18:21 2016 -0400
+++ b/test-data/grep_results2.html	Thu Jun 02 08:58:39 2016 -0400
@@ -290,17 +290,11 @@
 <body class="f9 b9">
 <pre>
 GCTATAG<span class="bold"><span class="f4">AAATGT</span></span>TAACATCGAATGTACATTATAAC
-<span class="f6">--</span>
 CAGCTAACAATC<span class="bold"><span class="f4">AAGCGT</span></span>TACAGATTAGCCCCCCCC
-<span class="f6">--</span>
 GAACTTGCGTAACGTACAAAAATGCAAGCA<span class="bold"><span class="f4">AAAAGT</span></span>
-<span class="f6">--</span>
 GCTCTGTTAATCTAGA<span class="bold"><span class="f4">AAATGT</span></span>GTCTCCCCCCCCCC
-<span class="f6">--</span>
 <span class="bold"><span class="f4">AATCGT</span></span>ATAGCTCGGGCCGGATACTAGTACACCCCC
-<span class="f6">--</span>
 GATATAGTGGATAACTAATGCTCCCCCAG<span class="bold"><span class="f4">AACTGT</span></span>T
-<span class="f6">--</span>
 GAACGGACTATAGCCGGTATCCAAACAT<span class="bold"><span class="f4">AAATGT</span></span>TC
 </pre>
 </body>
Binary file text_processing.tar.bz2 has changed
--- a/tool_dependencies.xml	Fri Mar 18 15:18:21 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="gnu_coreutils" version="8.22">
-        <repository changeset_revision="8b60cf3e0c07" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="gnu_awk" version="4.1.0">
-        <repository changeset_revision="0f0bdef2f686" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="gnu_grep" version="2.14">
-        <repository changeset_revision="ee751bc2c822" name="package_gnu_grep_2_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="gnu_sed" version="4.2.2-sandbox">
-        <repository changeset_revision="ae00df77b031" name="package_gnu_sed_4_2_2_sandbox" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="text_processing_perl_packages" version="1.0">
-        <install version="1.0">
-            <actions>
-                <action type="setup_perl_environment">
-                    <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="perl" version="5.18.1" />
-                    </repository>
-                   <!-- allow downloading and installing an Perl package from cpan.org-->
-                   <package>https://cpan.metacpan.org/authors/id/S/SA/SALVA/Sort-Key-1.33.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Needed perl packages.
-        </readme>
-    </package>
-</tool_dependency>