diff span.xml @ 6:70500fd87b60 draft

Advanced options: threads and memory configuration

--- a/span.xml	Wed Nov 21 06:29:41 2018 -0500
+++ b/span.xml	Wed Nov 21 10:31:58 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="span" name="SPAN" version="0.7.1.4518">
+<tool id="span" name="SPAN" version="0.7.1.4518a">
     <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
     <requirements>
         <requirement type="package" version="0.7.1.4518">package_span_jar</requirement>
@@ -11,27 +11,35 @@
     <command interpreter="python">
 #if str($action.action_selector) == "model"
     #if str($control_file) != 'None':
-        span_wrapper.py model_with_control
+        span_wrapper.py
+            "${advanced_options.memory}" "${advanced_options.threads}"
+            model_with_control
             "${genome_file.name}" "${genome_file}"
             "${treatment_file.name}" "${treatment_file}"
             "${control_file.name}" "${control_file}"
             "${bin}"
     #else
-        span_wrapper.py model_without_control
+        span_wrapper.py
+            "${advanced_options.memory}" "${advanced_options.threads}"
+            model_without_control
             "${genome_file.name}" "${genome_file}"
             "${treatment_file.name}" "${treatment_file}"
             "${bin}"
     #end if
 #else
     #if str($control_file) != 'None':
-        span_wrapper.py peaks_with_control
+        span_wrapper.py
+            "${advanced_options.memory}" "${advanced_options.threads}"
+            peaks_with_control
             "${genome_file.name}" "${genome_file}"
             "${treatment_file.name}" "${treatment_file}"
             "${control_file.name}" "${control_file}"
             "${bin}"
             "${action.fdr}" "${action.gap}"
     #else
-        span_wrapper.py peaks_without_control
+        span_wrapper.py
+            "${advanced_options.memory}" "${advanced_options.threads}"
+            peaks_without_control
             "${genome_file.name}" "${genome_file}"
             "${treatment_file.name}" "${treatment_file}"
             "${bin}"
@@ -57,21 +65,29 @@
                 <option value="peaks">Compute SPAN model and produce peaks file</option>
             </param>
             <when value="peaks">
-                <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr"
+                <param name="fdr" size="5" type="float" value="0.0001" min="0" label="FDR" argument="--fdr"
                        help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
                        SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
                        Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
                        Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
                        q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
-                <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap"
+                <param name="gap" size="3" type="integer" value="5" min="0" label="GAP" argument="--gap"
                        help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
                        Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
             </when>
         </conditional>
 
-        <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin"
+        <param name="bin" size="5" type="integer" value="200" min="50" label="Bin size" argument="--bin"
                help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
                Default value is 200bp, approximately the length of one nucleosome."/>
+
+        <section name="advanced_options" title="Advanced Options">
+            <param name="memory" size="6" type="integer" value="2048" min="1024"
+                   label="Memory limit in megabytes" help="Default value is 2048 megabytes"/>
+            <param name="threads" argument="--threads" size="2" type="integer" value="2" min="1"
+                   label="Threads number"
+                   help="Default value is 2 threads. SPAN utilizes both multithreading and specialized processor extensions like SSE2, AVX, etc."/>
+        </section>
     </inputs>
     <outputs>
         <data name="model.span" format="span" from_work_dir="*.span"