--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsf-call_wrapper.xml	Sun Apr 19 20:51:13 2015 +0900
@@ -0,0 +1,116 @@
+<tool id="bsf-call" name="bsf-call" version="1.0.0">
+  <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
+<!--
+  <version_command></version_command>
+-->
+
+  <requirements>
+    <requirement type="set_environment">TOOLDIR</requirement>
+  </requirements>
+
+  <command interpreter="perl">
+    bsf-call_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1} 
+
+    #if $reference.source=="indexed":
+      $reference.index.fields.path
+    #else if $reference.source=="history":
+      $reference.own_file
+    #else 
+
+    #end if
+
+    #if $read.end=="single-end"
+      $in 
+    #else if $read.end=="paired-end"
+      $in1 $in2
+    #else
+      
+    #end if
+  </command>
+
+  <inputs>
+    <conditional name="reference">
+      <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in genome index</option>
+        <option value="history">Use a genome from the history and build index</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select reference genome">
+          <options from_data_table="bsf-call_indexes">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
+      </when>
+    </conditional>
+
+    <conditional name="read">
+      <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
+        <option value="single-end">Single-end reads</option>
+        <option value="paired-end">Paired-end reads</option>
+      </param>
+      <when value="single-end">
+        <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
+      </when>
+      <when value="paired-end">
+        <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
+        <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
+      </when>
+    </conditional> 
+  </inputs>
+
+  <outputs>
+    <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
+    <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
+  </outputs>
+
+  <help>
+**bsf-call**
+
+Mapping bisulfite-seq reads and calling methylated cytosines
+
+------
+
+**Input format**
+
+Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file). 
+
+------
+
+**Output format**
+
+Output is a six-column tab-delimited file::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome label (e.g. chr1)
+  2   | genomic position (0-based)
+  3   | strand (+,-)
+  4   | mC context (CG, CHG, CHH)
+  5   | mC rate (float)
+  6   | read coverage
+
+------
+
+**Contact**
+
+Toutai Mituyama
+
+mituyama-toutai AT aist.go.jp
+  </help>
+
+  <citations>
+    <citation type="doi">10.1093/nar/gkt1373</citation>
+  </citations>
+
+</tool>
+
+<!--
+Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory. 
+ \${GALAXY_SLOTS:-4} 
+
+Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime). 
+-->