changeset 1:75dc30937969 draft

Deleted selected files

Binary file imp_exp/export.pl has changed

--- a/imp_exp/export.xml	Wed Jul 09 04:48:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-<tool id="export" name="Export" version="1.0.0">
-<description>to a Local File</description>
-<command interpreter="perl">export.pl $symlink $dest $logfile
-#for $i in $files
-${i.file} ${i.name}
-#end for
-</command>
-<inputs>
-    <param name="symlink" type="select" display="radio" label="Copy or symlink files?">
-        <option value="0">COPY the files so I may delete the files from Galaxy</option>
-        <option value="1">SYMLINK the files; I will not delete the files from Galaxy</option>
-    </param>
-    <param name="dest" type="text" size='120' value="/home/galaxy/galaxy-work/" label="Destination folder" help="Must be writable by Galaxy user" />
-	<repeat name="files" title="Files to export">
-		<param name="file" type="data" format="data" label="File"/>
-        <param name="name" type="text" size='20' value="" label="Name" />
-	</repeat>
-</inputs>
-<outputs>
-    <data name="logfile" format="txt" />
-</outputs>
-<help>
-**What it does**
-
-This tool allows staff to export files from Galaxy to a specified NFS path.
-
-The destination folder must be writable by the Galaxy user. It is suggested that you create a folder ~/dropbox and chmod 777 it.
-</help>
-</tool>

--- a/imp_exp/link_path.pl	Wed Jul 09 04:48:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/perl
-
-# INTERNAL USE ONLY!
-# THIS TOOLS IS WRITTEN BASED ON link_path.pl FROM US DOE Joint Genome Institute.
-# 2012-02-10 Yamanaka
-
-# THIS TOOL HAS BEEN DEPRECATED IN FAVOR OF THE galaxy_import.pl AND gcpd.pl METHOD
-# WHICH DON'T REQUIRE SETTING METADATA MANUALLY FOR EACH FILE.
-
-use strict;
-use File::Copy;
-
-# CONFIG
-my @allowed_paths = ('/');
-
-# ARGS
-my ($src, $dest, $symlink)=@ARGV;
-die("Absolute path required\n") unless $src =~ /^\//;
-die("Paths containing '..' are disallowed\n") if $src =~ /\/\.\.\//;
-my $ok=0;
-foreach my $dir (@allowed_paths) {
-    my $re="^$dir";
-    $re =~ s/\//\\\//g;
-    if ($src =~ /$re/) {
-        $ok=1;
-        last;
-    }
-}
-die("Not an allowed source path\n") unless $ok;
-
-# CP
-unlink($dest);
-if ($symlink) {
-    symlink($src, $dest);
-} else {
-    copy($src,$dest);
-}
-exit;

--- a/imp_exp/link_path.xml	Wed Jul 09 04:48:09 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<tool id="import" name="Import" version="1.0.0">
-<description>a Local File</description>
-<command interpreter="perl">link_path.pl $source $dest $symlink</command>
-<inputs>
-    <param name="source" type="text" size='100' value='' label="Complete pathname" />
-    <param name="symlink" type="select" display="radio" label="Is that a permanent location?">
-        <option value="0">No, COPY the file</option>
-        <option value="1">Yes, SYMLINK the file</option>
-    </param>
-</inputs>
-<outputs>
-    <data format="data" name="dest" />
-</outputs>
-<help>
-This tool allows you to import a local file into Galaxy.
-You have to edit the imported file's metadata to assign it to the appropriate datatype.
-</help>
-</tool>