# HG changeset patch
# User iuc
# Date 1430322916 14400
# Node ID a4bfde844a72608c0589602ee08623380fe3a5a5
# Parent  3ab2ac4f330442b1403cb88788c04c5fd3985762
Uploaded

diff -r 3ab2ac4f3304 -r a4bfde844a72 macros.xml
--- a/macros.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<macros>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="1.13">package_perl_xml_xpath</requirement>
-      <yield/>
-    </requirements>
-  </xml>
-  <token name="@WRAPPER_VERSION@">1.0</token>
-  <xml name="stdio">
-    <stdio>
-      <exit_code range="1:"/>
-      <exit_code range=":-1"/>
-      <regex match="Error:"/>
-      <regex match="Exception:"/>
-    </stdio>
-  </xml>
-  <token name="@ATTRIBUTION@"><![CDATA[
-**Attribution**
-
-This Galaxy tool relies on the ``xpath`` tool provided in `libxml-xpath-perl`
-by the Debian Maintainers.
-  ]]>
-  </token>
-</macros>
diff -r 3ab2ac4f3304 -r a4bfde844a72 test-data/1.xml
--- a/test-data/1.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-<b attr="value">1</b>
diff -r 3ab2ac4f3304 -r a4bfde844a72 test-data/2.xml
--- a/test-data/2.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-<b attr="value">1</b>
-<b attr="none">2</b>
diff -r 3ab2ac4f3304 -r a4bfde844a72 test-data/3.xml
--- a/test-data/3.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-1
-2
-3
diff -r 3ab2ac4f3304 -r a4bfde844a72 test-data/test.xml
--- a/test-data/test.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<root>
-    <a>
-        <b attr="value">1</b>
-        <b attr="none">2</b>
-        <b>3</b>
-    </a>
-    <c>
-        <d>4</d>
-        <d>5</d>
-    </c>
-</root>
-
diff -r 3ab2ac4f3304 -r a4bfde844a72 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="package_perl_xml_xpath" version="1.13">
-    <repository changeset_revision="18eb71d4fd93" name="package_perl_xml_xpath_1_13" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>
diff -r 3ab2ac4f3304 -r a4bfde844a72 xpath
--- a/xpath	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,201 +0,0 @@
-#!/usr/bin/perl -w
-eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
-    if 0; # not running under some shell
-use strict;
-
-$| = 1;
-
-use XML::XPath;
-
-my @paths;
-my $pipeline;
-my $SUFFIX = "\n";
-my $PREFIX = "";
-my $quiet = 0;
-
-
-PARSE: while ((@ARGV >= 1) && ($ARGV[0] =~ /^-./ )) {
-	OPTIONS: {
-		if ($ARGV[0] eq "-e") {
-			shift;
-			push @paths, shift;
-			last OPTIONS;
-		}
-		if ($ARGV[0] eq "-p") {
-			shift;
-			$PREFIX = shift;
-			last OPTIONS;
-		}
-		if ($ARGV[0] eq "-s") {
-			shift;
-			$SUFFIX = shift;
-			last OPTIONS;
-		}
-		if ($ARGV[0] eq "-q") {
-			$quiet = 1;
-			shift;
-			last OPTIONS;
-		}
-		print STDERR "Unknown option ignore: ", shift;
-	}
-}
-
-unless (@paths >= 1) {
-	print STDERR qq(Usage:
-$0 [options] -e query [-e query...] [filename...]
-
-	If no filenams are given, supply XML on STDIN.
-	You must provide at least one query. Each supplementary
-	query is done in order, the previous query giving the
-	context of the next one.
-
-	Options:
-
-	-q		quiet. Only output the resulting PATH
-	-s suffix	use suffix instead of linefeed.
-	-p postfix	use prefix instead of nothing.
-);
-	exit;
-}
-
-do
-{
-	my $xpath;
-	my @curpaths = @paths;
-	my $filename;
-	if (@ARGV >= 1) {
-		$filename = shift @ARGV;
-		$xpath = XML::XPath->new(filename => $filename);
-	}
-	else {
-		$filename = 'stdin';
-		$xpath = XML::XPath->new(ioref => \*STDIN);
-	}
-
-	my $nodes = $xpath->find(shift @curpaths);
-
-	if ($nodes->isa('XML::XPath::NodeSet')) {
-		while (@curpaths >= 1) {
-			$nodes = find_more($xpath, shift @curpaths, $nodes);
-			last unless $nodes->isa('XML::XPath::NodeSet');
-		}
-	}
-
-	if ($nodes->isa('XML::XPath::NodeSet')) {
-		if ($nodes->size) {
-			print STDERR "Found ", $nodes->size, " nodes in $filename:\n" unless $quiet;
-			foreach my $node ($nodes->get_nodelist) {
-				print STDERR "-- NODE --\n" unless $quiet;
-				print $PREFIX, $node->toString, $SUFFIX;
-			}
-		}
-		else {
-			print STDERR "No nodes found in $filename\n" unless $quiet;
-		}
-	}
-	else {
-		print STDERR "Query didn't return a nodeset. Value: ";
-		print $nodes->value, "\n";
-	}
-
-} until (@ARGV < 1);
-
-exit;
-
-sub find_more {
-	my $xpath = shift;
-	my $find = shift;
-	my ($nodes) = @_;
-
-	my $newnodes = XML::XPath::NodeSet->new;
-
-	foreach my $node ($nodes->get_nodelist) {
-		my $new = $xpath->find($find, $node);
-		if ($new->isa('XML::XPath::NodeSet')) {
-			$newnodes->append($new);
-		}
-		else {
-			warn "Not a nodeset: ", $new->value, "\n";
-		}
-	}
-
-	return $newnodes;
-}
-
-__END__
-
-=head1 NAME
-
-xpath - a script to query XPath statements in XML documents.
-
-=head1 SYNOPSIS
-
-B<xpath [-s suffix] [-p prefix] [-q] -e query [-e query] ... [file] ...>
-
-=head1 DESCRIPTION
-
-B<xpath> uses the L<XML::XPath|XML::XPath> perl module to make XPath queries
-to any XML document. The L<XML::XPath|XML::XPath> module aims to comply exactly
-to the XPath specification at C<http://www.w3.org/TR/xpath> and yet
-allows extensions to be added in the form of functions.
-
-The script takes any number of XPath pointers and tries to apply them
-to each XML document given on the command line. If no file arguments
-are given, the query is done using C<STDIN> as an XML document.
-
-When multiple queries exist, the result of the last query is used as
-context for the next query and only the result of the last one is output.
-The context of the first query is always the root of the current document.
-
-=head1 OPTIONS
-
-=head2 B<-q>
-
-Be quiet. Output only errors (and no separator) on stderr.
-
-=head2 B<-s suffix>
-
-Place C<suffix> at the end of each entry. Default is a linefeed.
-
-=head2 B<-p prefix>
-
-Place C<prefix> preceding each entry. Default is nothing.
-
-=head1 BUGS
-
-The author of this man page is not very fluant in english. Please,
-send him (L<fabien@tzone.org>) any corrections concerning this text.
-
-See also L<XML::XPath(3pm)>.
-
-=head1 SEE ALSO
-
-L<XML::XPath(3pm)>.
-
-=head1 HISTORY
-
-This module is copyright 2000 Fastnet Software Ltd. This is free
-software, and as such comes with NO WARRANTY. No dates are used in this
-module. You may distribute this module under the terms of either the
-Gnu GPL,  or under specific licencing from Fastnet Software Ltd.
-Special free licencing consideration will be given to similarly free
-software. Please don't flame me for this licence - I've put a lot of
-hours into this code, and if someone uses my software in their product
-I expect them to have the courtesy to contact me first.
-
-Full support for this module is available from Fastnet Software Ltd on
-a pay per incident basis. Alternatively subscribe to the Perl-XML
-mailing list by mailing lyris@activestate.com with the text:
-
-	SUBSCRIBE Perl-XML
-
-in the body of the message. There are lots of friendly people on the
-list, including myself, and we'll be glad to get you started.
-
-Matt Sergeant, matt@sergeant.org
-
-This man page was added as well as some serious modifications to the script
-by Fabien Ninoles <fabien@debian.org> for the Debian Project.
-
-=cut
-
diff -r 3ab2ac4f3304 -r a4bfde844a72 xpath.xml
--- a/xpath.xml	Tue Apr 28 22:56:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<?xml version="1.0"?>
-<tool id="xpath" name="XPath" version="@WRAPPER_VERSION@.0">
-  <description>compute xpath expressions on XML data</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command interpreter="bash"><![CDATA[xpath
-      -q
-      -e '$expression' $input > $output
-      ]]></command>
-  <inputs>
-    <param name="input" type="data" format="xml" label="Input XML data"/>
-    <param name="expression" type="text" label="XPath Query">
-      <sanitizer>
-        <valid>
-          <add value="&quot;"/>
-          <add value="["/>
-          <add value="]"/>
-          <add value="@"/>
-        </valid>
-      </sanitizer>
-    </param>
-  </inputs>
-  <outputs>
-      <!-- TODO: sometimes there's text output (e.g. text() queries) -->
-    <data format="xml" name="output" label="XPath expression on $input.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="test.xml"/>
-      <param name="expression" value="//b[@attr=&quot;value&quot;]" />
-      <output name="output" file="1.xml"/>
-    </test>
-    <test>
-      <param name="input" value="test.xml"/>
-      <param name="expression" value="//b[@attr]" />
-      <output name="output" file="2.xml"/>
-    </test>
-    <test>
-      <param name="input" value="test.xml"/>
-      <param name="expression" value="//b/text()" />
-      <output name="output" file="3.xml"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-**What it does**
-
-Query XML files with XPath expressions.
-
-For an example input file::
-
-    <root>
-        <IdList>
-            <Id>1234</Id>
-            <Id>1235</Id>
-            <Id>1236</Id>
-            <Id>1237</Id>
-        </IdList>
-    </root>
-
-One could query out the IDs specifically with a query like::
-
-    //Id/text()
-
-**XPath Expressions**
-
-There are many helpful tutorials on the internet for XPath expressions.
-`Wikipedia <https://en.wikipedia.org/wiki/XPath>`__ has a number of good
-examples.
-
-**Some More Examples**
-
-For an XML document like the following::
-
-    <root>
-        <a>
-            <b attr="value">1</b>
-            <b attr="none">2</b>
-            <b>3</b>
-        </a>
-        <c>
-            <d>4</d>
-            <e>5</e>
-        </c>
-    </root>
-
-Here are some example queries and their outputs:
-
-+====================+===================================================+
-| Query              | Result                                            |
-+--------------------+---------------------------------------------------+
-| //b[@attr="value"] | <b attr="value">1</b>                             |
-+--------------------+---------------------------------------------------+
-| //b[@attr]         | <b attr="value">1</b><b attr="none">2</b>         |
-+--------------------+---------------------------------------------------+
-| //b                | <b attr="value">1</b><b attr="none">2</b><b>3</b> |
-+--------------------+---------------------------------------------------+
-| //b/text()         | 1\n2\n3                                           |
-+--------------------+---------------------------------------------------+
-| /root/*/*/text()   | 1\n2\n3\n4\n5                                     |
-+--------------------+---------------------------------------------------+
-
-
-
-@ATTRIBUTION@
-]]></help>
-</tool>