diff export2sam.xml @ 0:61f3089ddc74 default tip

commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export2sam.xml	Tue Dec 30 18:53:23 2014 +0900
@@ -0,0 +1,33 @@
+<tool id="export2sam" name="Export to SAM" version="0.1">
+  <description></description>
+  <parallelism method="basic"></parallelism>
+  <command interpreter="sh">
+    export2sam.sh
+      -a $read1
+      #if $pairCondition.pairSelect == "yes"
+        -b $read2
+      #end if
+      -o $output
+      $gunzip
+      $remove
+  </command>
+  <inputs>
+    <param name="read1" type="data" format="eland_export" label="ELAND export file" help="" />
+    <param name="gunzip" type="boolean" truevalue="-g" falsevalue="" checked="True" label="Input file is gzipped" help="" />
+    <param name="remove" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Remove (chr).fa and chr_fragments.fa/" help="" />
+    <conditional name="pairCondition">
+      <param name="pairSelect" type="select" label="Pair end?">
+        <option value="yes">Yes</option>
+        <option value="no" selected="True">No</option>
+      </param>
+      <when value="yes">
+        <param name="read2" type="data" format="eland_export" label="ELAND export file" help="" />
+      </when>
+      <when value="no"></when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="sam" name="output" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <help>If thou thyself canst do it, attend no other's help or hand.</help>
+</tool>