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Changeset 0:7e01c6a6dbed (2016-06-10)

Next changeset 1:1ba5c66e39c9 (2016-06-25)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath commit e0575333e6f08ef02fc66c2764b43ebd15c6b04b

added:
macros.xml
test-data/1.xml
test-data/2.xml
test-data/3.xml
test-data/test.xml
tool_dependencies.xml
xpath
xpath.xml

diff -r 000000000000 -r 7e01c6a6dbed macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jun 10 15:08:32 2016 -0400

[

@@ -0,0 +1,25 @@
+<?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 000000000000 -r 7e01c6a6dbed test-data/1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.xml Fri Jun 10 15:08:32 2016 -0400

@@ -0,0 +1,1 @@
+1

diff -r 000000000000 -r 7e01c6a6dbed test-data/2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.xml Fri Jun 10 15:08:32 2016 -0400

@@ -0,0 +1,2 @@
+1
+2

diff -r 000000000000 -r 7e01c6a6dbed test-data/3.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.xml Fri Jun 10 15:08:32 2016 -0400

@@ -0,0 +1,3 @@
+1
+2
+3

diff -r 000000000000 -r 7e01c6a6dbed test-data/test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.xml Fri Jun 10 15:08:32 2016 -0400

@@ -0,0 +1,12 @@
+<root>
+ <a>
+ 1
+ 2
+ 3
+ </a>
+ <c>
+ <d>4</d>
+ <d>5</d>
+ </c>
+</root>
+

diff -r 000000000000 -r 7e01c6a6dbed tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 10 15:08:32 2016 -0400

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+ <package name="package_perl_xml_xpath" version="1.13">
+ <repository changeset_revision="b0e8fcff8c27" name="package_perl_xml_xpath_1_13" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+ </package>
+</tool_dependency>

diff -r 000000000000 -r 7e01c6a6dbed xpath
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xpath Fri Jun 10 15:08:32 2016 -0400

[

@@ -0,0 +1,201 @@
+#!/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 000000000000 -r 7e01c6a6dbed xpath.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xpath.xml Fri Jun 10 15:08:32 2016 -0400

[

@@ -0,0 +1,111 @@
+<?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="""/>
+ <add value="["/>
+ <add value="]"/>
+ <add value="@"/>
+ </valid>
+ </sanitizer>
+ </param>
+ </inputs>
+ <outputs>
+ 
+ <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="value"]" />
+ <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>
+ 1
+ 2
+ 3
+ </a>
+ <c>
+ <d>4</d>
+ <e>5</e>
+ </c>
+ </root>
+
+Here are some example queries and their outputs:
+
++====================+===================================================+
+| Query | Result |
++--------------------+---------------------------------------------------+
+| //b[@attr="value"] | 1 |
++--------------------+---------------------------------------------------+
+| //b[@attr] | 12 |
++--------------------+---------------------------------------------------+
+| //b | 123 |
++--------------------+---------------------------------------------------+
+| //b/text() | 1\n2\n3 |
++--------------------+---------------------------------------------------+
+| /root/*/*/text() | 1\n2\n3\n4\n5 |
++--------------------+---------------------------------------------------+
+
+
+
+@ATTRIBUTION@
+]]></help>
+ <citations>
+ </citations>
+</tool>