# HG changeset patch
# User wolma
# Date 1418509211 18000
# Node ID e2b5f503e7b85690ba35308287757ff603851f49
Imported from capsule None
diff -r 000000000000 -r e2b5f503e7b8 convert.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/convert.xml Sat Dec 13 17:20:11 2014 -0500
@@ -0,0 +1,136 @@
+
+ between different sequence data formats
+
+ mimodd
+
+ mimodd version -q
+
+ mimodd convert
+
+ #for $i in $mode.input_list
+ ${i.file1}
+ #if $str($mode.iformat) in ("fastq_pe", "gz_pe"):
+ ${i.file2}
+ #end if
+ #end for
+ #if $str($mode.header) != "None":
+ --header $(mode.header)
+ #end if
+ --ofile $outputname
+ --iformat $(mode.iformat)
+ --oformat $(mode.oformat)
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+.. class:: infomark
+
+ **What it does**
+
+The tool converts between different file formats used for storing next-generation sequencing data.
+
+As input file types it can handle uncompressed or gzipped fastq, SAM or BAM format, which it can convert to SAM or BAM format.
+
+**Notes:**
+
+1) In its standard configuration Galaxy will decompress any .gz files during their upload, so the option to align gzipped fastq input is useful only with customized Galaxy instances or by using linked files as explained in our `recipe for using gzipped fastq files in Galaxy`_ from the `MiModD user guide`_.
+
+2) The tool can convert fastq files representing data from paired-end sequencing runs to appropriate SAM/BAM format provided that the mate information is split over two fastq files in corresponding order.
+
+ **TIP:** If your paired-end data is arranged differently, you may look into the *fastq splitter* and *fastq de-interlacer* tools for Galaxy from the `Fastq Manipulation category`_ of the Galaxy Tool Shed to see if they can convert your files to the expected format.
+
+3) Merging partial fastq (or gzipped fastq) files into a single SAM/BAM file is supported both for single-end and paired-end data. Simply add additional input datasets and select the appropriate files (pairs of files in case of paired-end data).
+
+ Concatenation of SAM/BAM file during conversion is currently not supported.
+
+4) For input in fastq format a SAM header file providing run metadata **has to be specified**. The information in this file will be used as the header data of the new SAM/BAM file. You can use the *NGS Run Annotation* tool to generate a new header file for your data.
+
+ For input in SAM/BAM format the tool will simply copy the existing header data to the new file. To modify the header of an existing SAM/BAM file, use the *Reheader BAM file* tool instead.
+
+.. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531
+.. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy
+.. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
+
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+
diff -r 000000000000 -r e2b5f503e7b8 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Dec 13 17:20:11 2014 -0500
@@ -0,0 +1,6 @@
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