--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_intervals.xml	Wed Sep 12 17:10:26 2012 -0400
@@ -0,0 +1,100 @@
+<tool id="gd_find_intervals" name="Find remarkable" version="1.0.0">
+  <description>genomic intervals</description>
+
+  <command interpreter="python">
+    find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
+
+    #if $override_metadata.choice == "0"
+      "$input.metadata.ref" "$input.metadata.rPos"
+    #else
+      "$override_metadata.ref_col" "$override_metadata.rpos_col"
+    #end if
+
+    "$score_col" "$shuffles"
+
+    #if $cutoff.type == 'percentage'
+      "$cutoff.cutoff_pct"
+    #else
+      "=$cutoff.cutoff_val"
+    #end if
+
+    "$out_format"
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Input">
+      <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
+    </param>
+
+    <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
+
+    <conditional name="cutoff">
+      <param name="type" type="select" label="Cutoff type">
+        <option value="percentage">percentage</option>
+        <option value="value">value</option>
+      </param>
+      <when value="percentage">
+        <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/>
+      </when>
+      <when value="value">
+        <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/>
+      </when>
+    </conditional>
+
+    <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
+
+    <param name="out_format" type="select" format="integer" label="Report SNPs">
+      <option value="0" selected="true">No</option>
+      <option value="1">Yes</option>
+    </param>
+
+    <conditional name="override_metadata">
+      <param name="choice" type="select" format="integer" label="Choose columns">
+        <option value="0" selected="true">No, get columns from metadata</option>
+        <option value="1" >Yes, choose columns</option>
+      </param>
+      <when value="0" />
+      <when value="1">
+        <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
+        <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output" format="interval">
+        <change_format>
+            <when input="out_format" value="1" format="bigwigpos" />
+        </change_format>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
+      <param name="score_col" value="5" />
+      <param name="type" value="value" />
+      <param name="cutoff_val" value="700.0" />
+      <param name="shuffles" value="10" />
+      <param name="out_format" value="0" />
+      <param name="choice" value="0" />
+
+      <output name="output" file="test_out/find_intervals/find_intervals.interval" />
+    </test>
+  </tests>
+
+  <help>
+**What it does**
+
+The user selects a SNP table and specifies the columns containing (1)
+chromosome, (2) position, (3) scores (such as an Fst-value for the SNP), (4)
+a percentage or raw score for the "cutoff" and (5) the number of times the
+data should be randomized (only intervals with score exceeding the maximum for
+the randomized data are reported).  If a percentage (e.g. 95%) is specified
+for #3, then that percentile of the scores is used as the cutoff; this may
+not work well if many SNPs have the same score.  The program subtracts the
+cutoff from every score, then finds genomic intervals (i.e., consecutive runs
+of SNPs) whose total score cannot be increased by adding or subtracting one
+or more SNPs at the ends of the interval.
+  </help>
+</tool>