# HG changeset patch
# User alermine
# Date 1339163238 14400
# Node ID 6b590f108b48c184b6ad5162ed72fbe360600453

Uploaded

diff -r 000000000000 -r 6b590f108b48 upload_local_file/upload_local_file.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/upload_local_file/upload_local_file.sh	Fri Jun 08 09:47:18 2012 -0400
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+#################################################################################################
+# Upload_local_file tool for Galaxy                                                             #
+# Allow users to add data in their histories whitout having to upload them through the network  #
+# - Script by Alban Lermine, Institut Curie 2012 -                                              #
+#################################################################################################
+
+
+while getopts "b:o:" optionName; do
+case "$optionName" in
+
+b) INPUT_FILE="$OPTARG";;
+o) DATASET="$OPTARG";;
+
+esac
+done
+
+rm $DATASET
+
+ln -s $INPUT_FILE $DATASET
diff -r 000000000000 -r 6b590f108b48 upload_local_file/upload_local_file.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/upload_local_file/upload_local_file.xml	Fri Jun 08 09:47:18 2012 -0400
@@ -0,0 +1,64 @@
+<tool id="upload_local_file" name="Upload local file">
+  <description>to current History</description>
+  <command interpreter="bash">upload_local_file.sh -b $file -o $out</command>
+  <inputs>
+    <param name="name" type="text" label="File Name"/>
+    <param name="extension" type="select" label="File type">
+	<option value="bam">Bam</option>
+    	<option value="txt">Text</option>
+	<option value="fastq">Fastq</option>
+	<option value="csfasta">Csfasta</option>
+	<option value="qual">Qual</option>
+	<option value="bed">Bed</option>
+	<option value="gff">Gff</option>
+	<option value="pdf">Pdf</option>
+	<option value="vcf">VCF</option>
+	<option value="sam">Sam</option>
+	<option value="fasta">Fasta</option>
+	<option value="xsq">Xsq</option>
+    </param>
+    <param name="file" type="text" size="30" label="Path to file">
+    <validator type="empty_field" message="You must specify a file path"/>
+    </param>
+    <param name="dbkey" type="genomebuild" label="Genome" />
+  </inputs>
+  <outputs>
+    <data format="bam" name="out" label="${name}.${extension}">
+	<change_format>
+		<when input="extension" value="txt" format="txt" />
+		<when input="extension" value="fastq" format="fastq" />
+		<when input="extension" value="csfasta" format="csfasta" />
+		<when input="extension" value="qual" format="qual" />
+		<when input="extension" value="bed" format="bed" />
+		<when input="extension" value="gff" format="gff" />
+		<when input="extension" value="vcf" format="vcf" />
+		<when input="extension" value="sam" format="sam" />
+		<when input="extension" value="fasta" format="fasta" />
+		<when input="extension" value="pdf" format="pdf" />
+		<when input="extension" value="xsq" format="xsq" />
+	</change_format>
+    </data>
+
+  </outputs>
+  <help>
+.. class:: infomark
+
+**What it does:**
+
+This tool allows users to add data in their histories whitout having to upload them through the network.
+
+------
+
+**Input:**
+
+You must provide a filename whitout the extension (which is provide by file type) and the path to the data on the server. If you don't find the extension of your file, don't panic, just upload it with the text extension, and then search for the good format by clicking on the pencil on the dataset created. 
+
+**Output:**
+
+Create the galaxy dataset corresponding to your file on servers.
+
+.. class:: infomark
+
+**Feedback**: alban.lermine@curie.fr
+  </help>
+</tool>