diff bamsort.xml @ 3:d6ec32ce882b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamsort.xml	Tue Mar 28 04:34:04 2017 -0400
@@ -0,0 +1,52 @@
+<tool id="bamsort" name="Sort BAM file" version="0.1.7.3">
+  <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command>mimodd version -q</version_command>
+  <command>
+	mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
+  </command>
+  
+  <inputs>
+    <conditional name="input">
+      <param label="Input data format" name="iformat" type="select">
+        <option value="bam">bam</option>
+        <option value="sam">sam</option>
+      </param>
+      <when value="bam">
+        <param format="bam" label="BAM input file to sort" name="ifile" type="data" />
+      </when>
+      <when value="sam">
+        <param format="sam" label="SAM input file to sort" name="ifile" type="data" />
+      </when>
+    </conditional>
+    <param label="Output format for the sorted data" name="oformat" type="select">
+      <option value="bam">bam</option>
+      <option value="sam">sam</option>
+    </param>
+    <param checked="false" falsevalue="" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." label="Sort by read names instead of coordinates" name="by_name" truevalue="-n" type="boolean" />
+  </inputs>
+  
+  <outputs>
+    <data format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}" name="output">
+      <change_format>
+	 <when format="sam" input="oformat" value="sam" />
+      </change_format>
+    </data>
+  </outputs>
+
+<help>
+.. class:: infomark
+
+   **What it does**
+
+The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
+
+Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order.
+
+The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
+
+</help>
+</tool>