diff galaxy-tools/biobank/tools/convert_sam.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/convert_sam.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,40 @@
+<tool id="vl_tools_convert_sam" name="VLT.convert_sam">
+  <description>converter</description>
+  <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=convert_sam.py
+    --logfile ${log_file} convert_sam -i ${input_file}
+    -o ${output_file} --reftag ${dbkey} --output-format ${output_type}
+    ## FIXME: find a way to import the default from the relevant module
+    --flank-size 125
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="sam" label="SAM input file" />
+    <param name="output_type" type="select" label="Convert to:">
+      <option value="marker_alignment">VL marker alignment</option>
+      <option value="segment_extractor">Genome segment extractor</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="output_file">
+      <change_format>
+        <when input="output_type" value="marker_alignment" format="tabular" />
+        <when input="output_type" value="segment_extractor" format="interval" />
+      </change_format>
+    </data>
+    <data format="txt" name="log_file" label="${tool.name}.log_file"/>
+  </outputs>
+  <help>
+**What it does**
+
+This tool converts SAM alignment data to VL marker alignment or Galaxy
+extract genomic DNA input.
+
+Expects single-end BWA alignment data produced by the previous steps
+in the workflow (see markers_to_fastq).
+
+**NOTE:** if the marker_alignment output format is selected, the
+Database/Build property must be set in the input SAM file.
+  </help>
+</tool>