# HG changeset patch
# User bgruening
# Date 1456507374 18000
# Node ID c78b1767db2b574eb2a8e23768f91306efee6081
# Parent  d9819ccb9ca77d774295447a421a50adfbe19510
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty

diff -r d9819ccb9ca7 -r c78b1767db2b cat.xml
--- a/cat.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/cat.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -20,7 +20,7 @@
     <inputs>
         <param name="inputs" multiple="true" type="data" format="txt" label="Datasets to concatenate"/>
         <repeat name="queries" title="Dataset">
-            <param name="inputs2" type="data" multiple="True" label="Select" />
+            <param name="inputs2" type="data" format="txt" multiple="True" label="Select" />
         </repeat>
     </inputs>
     <outputs>
diff -r d9819ccb9ca7 -r c78b1767db2b cut.xml
--- a/cut.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/cut.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -1,5 +1,5 @@
 <tool id="tp_cut_tool" name="Cut" version="@BASE_VERSION@.0">
-    <description>columns from a table</description>
+    <description>columns from a table (cut)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -43,7 +43,7 @@
                 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
             </when>
             <when value="-c">
-                <param name="list" type="text" size="20" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
+                <param name="list" type="text" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
                     <sanitizer>
                         <valid initial="string.printable">
                             <remove value="&apos;"/>
@@ -52,7 +52,7 @@
                 </param>
             </when>
             <when value="-b">
-                <param name="list" type="text" size="20" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
+                <param name="list" type="text" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
                     <sanitizer>
                         <valid initial="string.printable">
                             <remove value="&apos;"/>
diff -r d9819ccb9ca7 -r c78b1767db2b easyjoin.xml
--- a/easyjoin.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/easyjoin.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -44,7 +44,7 @@
             label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." />
         <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue=""
             label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." />
-        <param name="empty_string_filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
+        <param name="empty_string_filler" type="text" value="0" label="Value to put in unpaired (empty) fields">
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
diff -r d9819ccb9ca7 -r c78b1767db2b find_and_replace.xml
--- a/find_and_replace.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/find_and_replace.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -21,14 +21,14 @@
     </command>
     <inputs>
         <param name="infile" format="txt" type="data" label="File to process" />
-        <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
+        <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
                 </valid>
             </sanitizer>
         </param>
-        <param name="replace_pattern" type="text" size="20" label="Replace with"
+        <param name="replace_pattern" type="text" label="Replace with"
             help="Use simple text, or $&amp; (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
             <sanitizer>
                 <valid initial="string.printable">
diff -r d9819ccb9ca7 -r c78b1767db2b grep.xml
--- a/grep.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/grep.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -13,7 +13,7 @@
             GREP_COLOR='1;34'
             grep
                 --color=always
-                -P
+                $regex_type
                 -A $lines_after
                 -B $lines_before
                 $invert
@@ -22,7 +22,7 @@
                 '${infile}' | $__tool_directory__/ansi2html.sh > "${output}"
         #else:
             grep
-                -P
+                $regex_type
                 -A $lines_after
                 -B $lines_before
                 $invert
@@ -41,8 +41,14 @@
             <option value="">Match</option>
             <option value="-v">Don't Match</option>
         </param>
-
-        <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
+        
+        <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">
                     <remove value="&apos;"/>
@@ -76,6 +82,7 @@
             <!-- grep a FASTA file for sequences with specific motif -->
             <param name="infile" value="grep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-P" />
             <param name="invert" value="" />
             <param name="url_paste" value="AA.{2}GT" />
             <param name="lines_before" value="1" />
@@ -88,6 +95,7 @@
              show highlighed output -->
             <param name="infile" value="grep1.txt" />
             <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-P" />
             <param name="invert" value="" />
             <param name="url_paste" value="AA.{2}GT" />
             <param name="lines_before" value="0" />
@@ -95,6 +103,28 @@
             <param name="color" value="COLOR" />
             <output name="output" file="grep_results2.html" />
         </test>
+        <test><!-- tests egrep -->
+            <param name="infile" value="egrep1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-E" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="[^ ]+" />
+            <param name="lines_before" value="0" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="NOCOLOR" />
+            <output name="output" file="egrep_results1.txt" />
+        </test>
+        <test><!-- same regex as egrep test, but different outcome with basic regex -->
+            <param name="infile" value="egrep1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="regex_type" value="-G" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="[^ ]+" />
+            <param name="lines_before" value="0" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="NOCOLOR" />
+            <output name="output" file="egrep_results2.txt" />>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r d9819ccb9ca7 -r c78b1767db2b head.xml
--- a/head.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/head.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -20,7 +20,7 @@
             <option value="">Keep first lines</option>
             <option value="-">Remove last lines</option>
         </param>
-        <param name="count" type="integer" size="5" value="10"
+        <param name="count" type="integer" value="10"
             label="Number of lines" help="These will be kept/discarded depending on 'operation'. (--lines)" />
     </inputs>
     <outputs>
diff -r d9819ccb9ca7 -r c78b1767db2b multijoin.xml
--- a/multijoin.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/multijoin.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -36,7 +36,7 @@
         <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" />
         <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" />
         <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." />
-        <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
+        <param name="filler" type="text" value="0" label="Value to put in unpaired (empty) fields">
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
diff -r d9819ccb9ca7 -r c78b1767db2b recurring_lines.xml
--- a/recurring_lines.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/recurring_lines.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -19,7 +19,7 @@
     </command>
     <inputs>
         <repeat name="token_set" title=" selection" min="1">
-            <param name="line" type="text" size="30"
+            <param name="line" type="text"
                 label="Characters to insert" help="Specify the characters that will be inserted X times in every line"/>
             <conditional name="repeat_select">
                 <param name="repeat_select_opts" type="select" label="Specify the number of iterations by">
@@ -27,7 +27,7 @@
                     <option value="user" selected="True">User defined number</option>
                 </param>
                 <when value="user">
-                    <param name="times" size="10" type="integer" value="10" min="1" label="How many times?"/>
+                    <param name="times" type="integer" value="10" min="1" label="How many times?"/>
                 </when>
                 <when value="file">
                     <param name="infile" type="data" format="txt" label="Template file"
diff -r d9819ccb9ca7 -r c78b1767db2b replace_text_in_column.xml
--- a/replace_text_in_column.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/replace_text_in_column.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -21,14 +21,14 @@
         <param format="tabular" name="infile" type="data" label="File to process" />
         <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
 
-        <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
+        <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
                 </valid>
             </sanitizer>
         </param>
-        <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
+        <param name="replace_pattern" type="text" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
diff -r d9819ccb9ca7 -r c78b1767db2b replace_text_in_line.xml
--- a/replace_text_in_line.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/replace_text_in_line.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -19,14 +19,14 @@
     </command>
     <inputs>
         <param format="txt" name="infile" type="data" label="File to process" />
-         <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
+         <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
                 </valid>
             </sanitizer>
         </param>
-         <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
+         <param name="replace_pattern" type="text" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
diff -r d9819ccb9ca7 -r c78b1767db2b sort.xml
--- a/sort.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/sort.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -26,7 +26,7 @@
     </command>
     <inputs>
         <param format="tabular" name="infile" type="data" label="Sort Query" />
-        <param name="header" type="integer" size="5" value="0"
+        <param name="header" type="integer" value="0"
             label="Number of header lines" help="These will be ignored during sort.">
             <validator type="in_range" message="Negative values are not allowed." min="0"/>
         </param>
diff -r d9819ccb9ca7 -r c78b1767db2b sorted_uniq.xml
--- a/sorted_uniq.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/sorted_uniq.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -64,7 +64,7 @@
 
         <param name="ignorecase" type="boolean" truevalue="-i" falsevalue=""
             label="Ignore differences in case when comparing" help="(-i)"/>
-        <param name="skipfields" type="integer" size="2" value="0"
+        <param name="skipfields" type="integer" value="0"
             label="Avoid comparing the first N fields" help="Use zero to start from the first field. (-f)" />
     </inputs>
     <outputs>
diff -r d9819ccb9ca7 -r c78b1767db2b tac.xml
--- a/tac.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/tac.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -32,7 +32,7 @@
                     label="Attach the separator before instead of after" help="(--before)"/>
                 <param name="regex" type="boolean" truevalue="-r" falsevalue="" checked="True"
                     label="Interpret the separator as a regular expression" help="(--regex)"/>
-                <param name="separator_string" size="5" type="text" value=""
+                <param name="separator_string" type="text" value=""
                     label="Separator to use" help="(--separator)" />
             </when>
         </conditional>
diff -r d9819ccb9ca7 -r c78b1767db2b tail.xml
--- a/tail.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/tail.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -19,7 +19,7 @@
             <option value="">Keep last lines</option>
             <option value="+">Keep everything from this line on</option>
         </param>
-        <param name="num_lines" type="integer" size="5" value="10"
+        <param name="num_lines" type="integer" value="10"
             label="Number of lines" help="These will be kept (depending on 'operation'). (--lines)" />
     </inputs>
     <outputs>
diff -r d9819ccb9ca7 -r c78b1767db2b test-data/egrep1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/egrep1.txt	Fri Feb 26 12:22:54 2016 -0500
@@ -0,0 +1,1 @@
+actgagctacg	agctacgatcg		atcgactacga
diff -r d9819ccb9ca7 -r c78b1767db2b test-data/egrep_results1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/egrep_results1.txt	Fri Feb 26 12:22:54 2016 -0500
@@ -0,0 +1,1 @@
+actgagctacg	agctacgatcg		atcgactacga
diff -r d9819ccb9ca7 -r c78b1767db2b test-data/egrep_results2.txt
diff -r d9819ccb9ca7 -r c78b1767db2b tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/tool_dependencies.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="gnu_coreutils" version="8.22">
-        <repository changeset_revision="b638666e399d" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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="440a5170003f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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="30b2e70d982e" name="package_gnu_grep_2_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3f6615b56ebb" 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="f6efd799dc70" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="318ccddfe301" 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="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="318ccddfe301" 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-->
diff -r d9819ccb9ca7 -r c78b1767db2b unfold_column.py
--- a/unfold_column.py	Tue Jun 30 17:47:36 2015 -0400
+++ b/unfold_column.py	Fri Feb 26 12:22:54 2016 -0500
@@ -4,11 +4,16 @@
 
 out = open(sys.argv[4], 'w+')
 
+sep = sys.argv[3]
+# un-sanitize Galaxy inputs
+if sep == 'X':
+    sep = ';'
+
 with open(sys.argv[1]) as handle:
     for line in handle:
         cols = line.split('\t')
         unfolding_column = int(sys.argv[2]) - 1
         column_content = cols[ unfolding_column ]
-        for elem in column_content.split( sys.argv[3] ):
+        for elem in column_content.split( sep ):
             out.write( '\t'.join( cols[:unfolding_column] + [elem] + cols[unfolding_column+1:]) )
 out.close()
diff -r d9819ccb9ca7 -r c78b1767db2b unfold_column.xml
--- a/unfold_column.xml	Tue Jun 30 17:47:36 2015 -0400
+++ b/unfold_column.xml	Fri Feb 26 12:22:54 2016 -0500
@@ -9,7 +9,7 @@
         unfold_column.py
             '${infile}'
             $column
-            "$delimiter"
+            "${delimiter}"
             '${outfile}'
 ]]>
     </command>
@@ -23,6 +23,7 @@
             <option value="-">Dash</option>
             <option value="_">Underscore</option>
             <option value="|">Pipe</option>
+            <option value=";">Semicolon</option>
         </param>
     </inputs>
     <outputs>