# HG changeset patch
# User wolma
# Date 1418509206 18000
# Node ID 37e44e7e2d508697741003e8386f7d9f750e0c81
Imported from capsule None
diff -r 000000000000 -r 37e44e7e2d50 sam_header.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_header.xml Sat Dec 13 17:20:06 2014 -0500
@@ -0,0 +1,128 @@
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+ Create a SAM format header from run metadata for sample annotation.
+
+ mimodd
+
+ mimodd version -q
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+ mimodd header
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+ --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
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+.. class:: infomark
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+ **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:**
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+**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.
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diff -r 000000000000 -r 37e44e7e2d50 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Dec 13 17:20:06 2014 -0500
@@ -0,0 +1,6 @@
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