diff tools/rtg/readsim.xml @ 1:8593828f91e7 default tip

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/readsim.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,75 @@
+<tool id="rtg_readsim" name="Simulate reads">
+  <description>with RTG readsim</description>
+  <command interpreter="bash">galaxy-rtg-wrapper.sh readsim
+-t ${input.extra_files_path}
+#if str($input2) != "None":
+-T ${input2.extra_files_path}
+#end if
+#if $limit.sType == "numreads":
+-n $limit.n
+#else
+-c $limit.c
+#end if
+-m $m
+-M $M
+--machine $machine.sMachine
+#if $machine.sMachine == "illumina_se":
+-r $machine.r
+#else if $machine.sMachine == "illumina_pe":
+-L $machine.L
+-R $machine.R
+#else if $machine.sMachine == "454_pe":
+--454-min-total-size $machine.454-min
+--454-max-total-size $machine.454-max
+#end if
+--seed $seed
+-o ${output.extra_files_path} >$output</command>
+  <inputs>
+
+    <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
+    <param name="input2" type="data" format="rtg_sdf" label="SDF with second genome for simulating diploid genomes" optional="true" />
+    <param name="m" type="integer" value="200" label="Minimum fragment length" help="Total number of reads"/>
+    <param name="M" type="integer" value="400" label="Minimum fragment length" help="Total number of reads"/>
+
+    <conditional name="limit">
+      <param name="sType" type="select" label="Select read limit">
+        <option value="numreads">Fixed number of reads</option>
+        <option value="coverage">Fixed coverage</option>
+      </param>
+      <when value="numreads">
+        <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/>
+      </when>
+      <when value="coverage">
+        <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/>
+      </when>
+    </conditional>	
+
+    <conditional name="machine">
+      <param name="sMachine" type="select" label="Select machine type">
+        <option value="illumina_pe">Illumina paired-end</option>
+        <option value="illumina_se">Illumina single-end</option>
+        <option value="454_pe">454 paired-end</option>
+      </param>
+      <when value="illumina_se">
+        <param name="r" type="integer" value="100" label="Read length" help="Target read length on left side"/>
+      </when>
+      <when value="illumina_pe">
+        <param name="L" type="integer" value="100" label="Left read length" help="Target read length on left side"/>
+        <param name="R" type="integer" value="100" label="Right read length" help="Target read length on right side"/>
+      </when>
+      <when value="454_pe">
+        <param name="454-min" type="integer" value="500" label="Minimum total length" help="Minimum sum of left and right read lengths"/>
+        <param name="454-max" type="integer" value="300" label="Maximum total length" help="Maximum sum of left and right read lengths"/>
+      </when>
+    </conditional>	
+    <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/>
+  </inputs>
+  <outputs>
+    <data format="rtg_sdf" name="output" />
+  </outputs>
+
+  <help>
+This tool creates an SDF containing randomly generated reads.
+  </help>
+
+</tool>