# HG changeset patch
# User wolma
# Date 1418160500 18000
# Node ID 7bce49512badc776d5419c9d80e477f789999a46
# Parent  623cf7b461fa6e21b9ad623230c917261ce5c0cd
version 0_1_5

diff -r 623cf7b461fa -r 7bce49512bad sam_header.xml
--- a/sam_header.xml	Thu Aug 14 10:36:08 2014 -0400
+++ b/sam_header.xml	Tue Dec 09 16:28:20 2014 -0500
@@ -1,42 +1,43 @@
-<tool id="sam_header" name="NGS Run Annotation">
+<tool id="ngs_run_annotation" name="NGS Run Annotation">
   <description>Create a SAM format header from run metadata for sample annotation.</description>
   <requirements>
-    <requirement type="package" version="0.1.3">mimodd</requirement>
+    <requirement type="package" version="0.1.5">mimodd</requirement>
   </requirements>
+  <version_command>mimodd version -q</version_command>
   <command>
   	mimodd header
 
-	--rg_id "$rg_id"
-	--rg_sm "$rg_sm"
+	--rg-id "$rg_id"
+	--rg-sm "$rg_sm"
 	
 	#if $str($rg_cn):
-		--rg_cn "$rg_cn"
+		--rg-cn "$rg_cn"
 	#end if
 	#if $str($rg_ds):
-		--rg_ds "$rg_ds"
+		--rg-ds "$rg_ds"
 	#end if	
-	#if $str($anno) and $str($month) and $str($day):
-		--rg_dt "$anno-$month-$day"
+	#if $str($rg_date):
+		--rg-dt "$rg_date"
 	#end if
 	#if $str($rg_lb):
-		--rg_lb "$rg_lb"
+		--rg-lb "$rg_lb"
 	#end if
 	#if $str($rg_pl):
-		--rg_pl "$rg_pl"
+		--rg-pl "$rg_pl"
 	#end if
-	#if $str($rg_ds):
-		--rg_pi "$rg_pi"
+	#if $str($rg_pi):
+		--rg-pi "$rg_pi"
 	#end if
 	#if $str($rg_pu):
-		--rg_pu "$rg_pu"
+		--rg-pu "$rg_pu"
 	#end if
 	
-	--outputfile $outputfile
+	--ofile $outputfile
 
   </command>
 
   <inputs>
-    <param name="rg_id" type="text" size="80" label="read-group ID (mandatory)">
+    <param name="rg_id" type="text" size="80" label="read-group ID (required)">
         <sanitizer invalid_char="">
             <valid initial="string.printable">
                 <remove value="&quot;" />
@@ -46,17 +47,7 @@
             </mapping>
         </sanitizer>
     </param>
-    <param name="rg_sm" type="text" size="80" label="sample name (mandatory)">
-        <sanitizer invalid_char="">
-            <valid initial="string.printable">
-                <remove value="&quot;" />
-            </valid>
-            <mapping initial="none">
-                <add source="&quot;" target="\&quot;"/>
-            </mapping>
-        </sanitizer>
-    </param>
-    <param name="rg_cn" type="text" size="80" label="name of sequencing center">
+    <param name="rg_sm" type="text" size="80" label="sample name (required)">
         <sanitizer invalid_char="">
             <valid initial="string.printable">
                 <remove value="&quot;" />
@@ -76,9 +67,17 @@
             </mapping>
         </sanitizer>
     </param>
-    <param name="anno" type="text" label="year (YYYY) the run was produced" />
-    <param name="month" type="text" label="month (MM) the run was produced" />
-    <param name="day" type="text" label="day (DD) the run was produced" />
+    <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" />
+    <param name="rg_cn" type="text" size="80" label="name of sequencing center">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove value="&quot;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&quot;" target="\&quot;"/>
+            </mapping>
+        </sanitizer>
+    </param>
     <param name="rg_lb" type="text" size="80" label="read-group library">
         <sanitizer invalid_char="">
             <valid initial="string.printable">
@@ -122,7 +121,7 @@
 
 **Tip:**
 
-While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, the **recommended approach** is to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming this practice protects against information loss and ensures that the input datasets will remain useful for others in the future.
+While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming, this practice protects against information loss and ensures that the input datasets will remain useful for others in the future.
 
 </help>
 </tool>