diff sam_header.xml @ 0:6231ae8f87b8

Uploaded
author wolma
date Wed, 11 Feb 2015 08:29:02 -0500
parents
children a548b3c6ed00
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_header.xml	Wed Feb 11 08:29:02 2015 -0500
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+<tool id="ngs_run_annotation" name="NGS Run Annotation">
+  <description>Create a SAM format header from run metadata for sample annotation.</description>
+  <version_command>mimodd version -q</version_command>
+  <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 $str($rg_date):
+		--rg-dt "$rg_date"
+	#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_pi):
+		--rg-pi "$rg_pi"
+	#end if
+	#if $str($rg_pu):
+		--rg-pu "$rg_pu"
+	#end if
+	
+	--ofile "$outputfile"
+
+  </command>
+
+  <inputs>
+    <param name="rg_id" type="text" size="80" label="read-group ID (required)">
+        <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 (required)">
+        <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="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">
+                <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, 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>
+