From 526c2507d7696779ab6272ae44c8085c84cf4a33 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <soranzo@crs4.it>
Date: Tue, 28 Oct 2014 12:21:00 +0100
Subject: [PATCH] dos2unix

---
 tools/filters/convert_characters.xml | 118 +++++++++++++--------------
 1 file changed, 59 insertions(+), 59 deletions(-)

diff --git a/tools/filters/convert_characters.xml b/tools/filters/convert_characters.xml
index 7d72e078513..9507f792d8d 100644
--- a/tools/filters/convert_characters.xml
+++ b/tools/filters/convert_characters.xml
@@ -1,59 +1,59 @@
-<tool id="Convert characters1" name="Convert">
-  <description>delimiters to TAB</description>
-  <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
-  <inputs>
-    <param name="convert_from" type="select" label="Convert all">
-      <option value="s">Whitespaces</option>
-      <option value="T">Tabs</option>
-      <!--<option value="Sp">Spaces</option>-->
-      <option value="Dt">Dots</option>
-      <option value="C">Commas</option>
-      <option value="D">Dashes</option>
-      <option value="U">Underscores</option>
-      <option value="P">Pipes</option>
-      <option value="Co">Colons</option>
-      <option value="Sc">Semicolons</option>
-    </param>
-    <param format="txt" name="input" type="data" label="in Dataset"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="1.bed"/>
-      <output name="out_file1" file="eq-convert.dat"/>
-    </test>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="a.txt"/>
-      <output name="out_file1" file="a.tab"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
-
------
-
-**Example**
-
-- Input file::
-
-    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
-    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
-    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
-    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
-
-- Converting all pipe delimiters of the above file to TABs will get::
-
-    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
-    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
-    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
-    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
-
-</help>
-</tool>
+<tool id="Convert characters1" name="Convert">
+  <description>delimiters to TAB</description>
+  <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
+  <inputs>
+    <param name="convert_from" type="select" label="Convert all">
+      <option value="s">Whitespaces</option>
+      <option value="T">Tabs</option>
+      <!--<option value="Sp">Spaces</option>-->
+      <option value="Dt">Dots</option>
+      <option value="C">Commas</option>
+      <option value="D">Dashes</option>
+      <option value="U">Underscores</option>
+      <option value="P">Pipes</option>
+      <option value="Co">Colons</option>
+      <option value="Sc">Semicolons</option>
+    </param>
+    <param format="txt" name="input" type="data" label="in Dataset"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="convert_from" value="s"/>
+      <param name="input" value="1.bed"/>
+      <output name="out_file1" file="eq-convert.dat"/>
+    </test>
+    <test>
+      <param name="convert_from" value="s"/>
+      <param name="input" value="a.txt"/>
+      <output name="out_file1" file="a.tab"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
+
+-----
+
+**Example**
+
+- Input file::
+
+    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
+    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
+    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
+    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
+
+- Converting all pipe delimiters of the above file to TABs will get::
+
+    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
+    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
+    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
+    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
+
+</help>
+</tool>