# HG changeset patch
# User wolma
# Date 1408024669 14400
# Node ID b2bc4e91846254191a141e03f8cc7d3128af6551

Uploaded

diff -r 000000000000 -r b2bc4e918462 sam_header.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_header.xml	Thu Aug 14 09:57:49 2014 -0400
@@ -0,0 +1,129 @@
+<tool id="sam_header" 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>
+  </requirements>
+  <command>
+  	mimodd header
+
+	--rg_id "$rg_id"
+	--rg_sm "$rg_sm"
+	
+	#if $str($rg_cn):
+		--rg_cn "$rg_cn"
+	#end if
+	#if $str($rg_ds):
+		--rg_ds "$rg_ds"
+	#end if	
+	#if $str($anno) and $str($month) and $str($day):
+		--rg_dt "$anno-$month-$day"
+	#end if
+	#if $str($rg_lb):
+		--rg_lb "$rg_lb"
+	#end if
+	#if $str($rg_pl):
+		--rg_pl "$rg_pl"
+	#end if
+	#if $str($rg_ds):
+		--rg_pi "$rg_pi"
+	#end if
+	#if $str($rg_pu):
+		--rg_pu "$rg_pu"
+	#end if
+	
+	--outputfile $outputfile
+
+  </command>
+
+  <inputs>
+    <param name="rg_id" type="text" size="80" label="read-group ID (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_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">
+        <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_ds" type="text" size="80" label="description">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove value="&quot;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&quot;" target="\&quot;"/>
+            </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_lb" type="text" size="80" label="read-group library">
+        <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_pl" type="text" label="platform/technology used to produce the reads" />
+    <param name="rg_pi" type="text" label="predicted median insert size" />
+    <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove value="&quot;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&quot;" target="\&quot;"/>
+            </mapping>
+        </sanitizer>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
+  </outputs>
+
+<help>
+.. class:: infomark
+
+   **What it does**
+
+This tool takes the user-provided information about a next-generation sequencing run and constructs a valid header in the SAM file format from it.
+
+The result file can be used by the tools *Convert* and *Reheader* or in the *SNAP Read Alignment* step to add run metadata to sequenced reads files (or to overwrite pre-existing information).
+
+**Note:**
+
+**MiModD requires run metadata for every input file at the Alignment step !**
+
+**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.
+
+</help>
+</tool>
+