# HG changeset patch
# User jetbrains
# Date 1542297889 18000
# Node ID 1f0c4f0a9c3b1e7c604f8a29a67f981449ea372a

Initial version of SPAN for ToolShed

diff -r 000000000000 -r 1f0c4f0a9c3b README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Nov 15 11:04:49 2018 -0500
@@ -0,0 +1,3 @@
+Release version
+===============
+Release is just a `span` snapshot from [https://github.com/JetBrains-Research/galaxy-applications](https://github.com/JetBrains-Research/galaxy-applications)
\ No newline at end of file
diff -r 000000000000 -r 1f0c4f0a9c3b span.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/span.xml	Thu Nov 15 11:04:49 2018 -0500
@@ -0,0 +1,69 @@
+<tool id="span" name="SPAN" version="0.7.1.4272">
+    <description>ChIP-Seq analysis</description>
+    <requirements>
+        <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
+        <!--<container type="docker">biolabs/span</container>-->
+    </requirements>
+    <stdio>
+        <!-- Wrapper ensures anything other than zero is an error -->
+        <exit_code range="1:"/>
+        <exit_code range=":-1"/>
+    </stdio>
+    <command interpreter="python">
+#if str($action.action_selector) == "model"
+    #if $control.control_selector
+        span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
+    #else
+        span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
+    #end if
+#else
+    #if $control.control_selector
+        span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+    #else
+        span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+    #end if
+#end if
+     </command>
+    <inputs>
+        <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
+               description="Treatment BAM reads to process"/>
+        <param name="genome" type="data" format="chrom.sizes" label="Genome chrom.sizes"
+               description="Genome build chrom.sizes file"/>
+
+        <conditional name="control">
+            <param name="control_selector" type="boolean" label="Control available" value="false"/>
+            <when value="true">
+                <param name="control_file" type="data" format="bam" label="Control BAM"
+                       description="Control BAM reads to process"/>
+            </when>
+        </conditional>
+
+        <conditional name="action">
+            <param name="action_selector" type="select" label="Action">
+                <option value="model">Compute SPAN model</option>
+                <option value="peaks">Compute SPAN model and produce peaks file</option>
+            </param>
+            <when value="model">
+                <param name="model_file" type="text" value="model.span" label="Model name"/>
+            </when>
+            <when value="peaks">
+                <param name="model_file" type="text" value="model.span" label="Model file name"/>
+                <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
+                <param name="gap" size="5" type="integer" value="5" label="GAP"/>
+                <param name="peaks_file" type="text" value="result.peak" label="Peaks file name"/>
+            </when>
+        </conditional>
+
+        <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
+    </inputs>
+    <outputs>
+        <data name="${action.model_file}" format="span" label="SPAN model file"/>
+        <data name="${action.peaks_file}" format="bed" label="SPAN peaks file">
+            <filter>action['action_selector'] == "peaks"</filter>
+        </data>
+    </outputs>
+    <help>
+        SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
+        Details: http://artyomovlab.wustl.edu/aging/span.html
+    </help>
+</tool>
diff -r 000000000000 -r 1f0c4f0a9c3b span_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/span_wrapper.py	Thu Nov 15 11:04:49 2018 -0500
@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import subprocess
+argv = sys.argv[1:]
+print 'Arguments {0}'.format(argv)
+
+SPAN_JAR = os.environ.get("SPAN_JAR")
+# span.jar from Docker container
+# SPAN_JAR = "/root/span.jar"
+print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
+
+# #if $action.action_selector
+#     #if str($control.control_selector) == "with_control"
+#         span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
+#     #else
+#         span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
+#     #end if
+# #else
+#     #if $control.control_selector
+#         span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+#     #else
+#         span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+#     #end if
+# #end if
+
+# See http://artyomovlab.wustl.edu/aging/span.html for command line options
+action = argv[0]
+control = argv[1]
+if action == 'model':
+    if control == 'with_control':
+        (chrom_sizes, treatment_file, bin, model_file, control_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, control_file, bin
+        )
+        print "MODEL FILE" + model_file
+    elif control == 'without_control':
+        (chrom_sizes, treatment_file, bin, model_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format(
+            SPAN_JAR, argv[2], argv[3], argv[4]
+        )
+        print "MODEL FILE" + model_file
+    else:
+        raise Exception("Unknown control option {}".format(control))
+
+elif action == "peaks":
+    if control == 'with_control':
+        (chrom_sizes, treatment_file, bin, model_file, control_file, fdr, gap, peaks_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, control_file, bin, fdr, gap, peaks_file
+        )
+        print "MODEL FILE" + model_file
+    elif control == 'without_control':
+        (chrom_sizes, treatment_file, bin, model_file, fdr, gap, peaks_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {} --fdr {} --gap {} --peaks {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, bin, fdr, gap, peaks_file
+        )
+        print "MODEL FILE" + model_file
+    else:
+        raise Exception("Unknown control option {}".format(control))
+else:
+    raise Exception("Unknown action command {}".format(action))
+
+
+print 'Launching SPAN: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)
diff -r 000000000000 -r 1f0c4f0a9c3b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Nov 15 11:04:49 2018 -0500
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!--
+    Package for downloading latest successful development tools.
+    https://galaxyproject.org/toolshed/tool-dependencies-tag-sets/
+    -->
+    <package name="package_span_jar" version="0.7.1.4272" prior_installation_required="True">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://download.jetbrains.com/biolabs/span/span-0.7.1.4272.jar</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/</destination_directory>
+                </action>
+                <!-- Set environment variable $INTEGRATION_JAR so Python script knows where to look -->
+                <action type="set_environment">
+                    <environment_variable name="$SPAN_JAR" action="set_to">$INSTALL_DIR/span-0.7.1.4272.jar</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Downloads SPAN Semi-supervised Peak Analyzer jar distribution file.
+        </readme>
+    </package>
+</tool_dependency>