# HG changeset patch
# User refinery-platform
# Date 1519326843 18000
# Node ID b87749d7a24c3b4388f9ece3683156803bd41f28
# Parent  5b28174e774dba8b5dced917034f79b632f6ca90
planemo upload commit 4fb0a789956149e5a58f4e370d7fe14f4e8bcf79

diff -r 5b28174e774d -r b87749d7a24c refinery_file_splitter.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/refinery_file_splitter.py	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+'''
+Test tool for splitting output files from Refinery Test Tools
+
+@author: Scott Ouellette
+
+Input: one text file
+Output: N output files based on the amount of input files that 
+got concatenated from Refinery test tool runs
+
+Requires Python v2.7
+
+'''
+
+import re
+import argparse
+
+
+def main(args):
+    create_many_files(args.input_file)
+
+
+def create_many_files(input_file):
+    # Split file's content when we see data that wasn't added by test tool runs
+    file_content = re.split("Output.*|Input.*", input_file.read())
+
+    sanitized_data = [
+        data.lstrip("\n") for data in file_content if data.rstrip("\n")]
+
+    # Create N ouput files based on the number of inputs run through test tools
+    for num, file_content in enumerate(sanitized_data):
+        open("Output file {}.txt".format(num + 1), 'w').write(file_content)
+
+
+if __name__ == '__main__':
+    version = "%(prog)s 0.1"
+    description = "Test tool for running workflows on Galaxy platform from Refinery"
+    parser = argparse.ArgumentParser(description=description, version=version)
+
+    parser.add_argument('-i', '--in-file', dest='input_file',
+                        type=file, metavar='INPUT_FILE', required=True,
+                        help='name of the input file')
+
+    # check argument values for errors
+    try:
+        args = parser.parse_args()
+    except IOError as e:
+        parser.error(e)
+
+    main(args)
diff -r 5b28174e774d -r b87749d7a24c refinery_test_1-N.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/refinery_test_1-N.xml	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,54 @@
+<?xml version='1.0' encoding='utf-8'?>
+
+<tool id="refinery_test_1-N" name="Refinery test tool 1-N" version="0.1">
+    <description>for testing Galaxy workflow execution from Refinery</description>
+        <command>
+            <![CDATA[ 	
+                ## Run the splitter tool upon a single input producing N outputs based on how many concatenated files our input was created from.
+                $__tool_directory__/refinery_file_splitter.py -i $input_file
+            ]]>
+        </command>  
+    <inputs>
+        <param name="input_file" format="txt" type="data" label="Input file"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="report">
+            <discover_datasets pattern="__designation_and_ext__" visible="true"/>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="concat_output.txt"/>
+            <discovered_dataset designation="Output file 1" ftype="txt">
+                <assert_contents>
+                    <has_line line="Contents of File 1:"/>
+                </assert_contents>
+            </discovered_dataset>
+            <discovered_dataset designation="Output file 2" ftype="txt">
+                <assert_contents>
+                    <has_line line="Contents of File 2:"/>
+                </assert_contents>
+            </discovered_dataset>
+            <discovered_dataset designation="Output file 3" ftype="txt">
+                <assert_contents>
+                    <has_line line="Contents of File 3:"/>
+                </assert_contents>
+            </discovered_dataset>
+        </test>
+    </tests>
+    <help>
+        .. class:: infomark
+
+        **Purpose**
+
+        To test Galaxy workflow execution and monitoring from Refinery.
+
+        -----
+
+        .. class:: infomark
+
+        **Inputs and outputs**
+
+        This wrapper will accept one input file with the concatenated data of N input files run through refinery test tools and will partition said data into N output files containing the afforementioned N input files original contents
+    </help>	
+</tool>
diff -r 5b28174e774d -r b87749d7a24c refinery_test_N-1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/refinery_test_N-1.xml	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='utf-8'?>
+
+<tool id="refinery_test_N-1" name="Refinery test tool N-1" version="0.1">
+    <description>for testing Galaxy workflow execution from Refinery</description>
+    <command>
+        <![CDATA[
+            ## Argparse expects many values for a single arg to be in the form of: -i INUPT INPUT1 INPUT2 ...
+            #set $inputs = " ".join([$input_file.__str__ for $input_file in $input_col])
+
+            ## Run the test tool with the N inputs from our Dataset Collection
+            $__tool_directory__/refinery_test_tool.py -i $inputs -o $output_file -e $exit_code -p $p_fail -s $sleep_time $stdout $stderr $empty_outfile
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_col" type="data_collection" collection_type="list" label="Input file"/>
+        <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
+        <param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
+        <param name="p_fail" type="float" label="Probability of failure [0.0, 1.0]" value="0.0" min="0.0" max="1.0"/>
+        <param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
+        <param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
+        <param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output_file" label="Refinery Test Tool N-1 Output" />
+    </outputs>
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+        <regex match=".+" source="stdout" level="fatal" description="Tool produced output to standard out" />
+        <regex match=".+" source="stderr" level="fatal" description="Tool produced output to standard error" />
+    </stdio>
+	<tests>
+  		<test>
+			<param name="input_col">
+            	<collection type="list">
+                	<element name="1" value="file1.txt"/>
+                	<element name="2" value="file2.txt"/>
+                	<element name="3" value="file3.txt"/>
+            	</collection>
+        	</param>
+			<param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
+        	<param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
+        	<param name="p_fail" type="float" label="Probability of failure [0.0, 1.0]" value="0.0" min="0.0" max="1.0"/>
+        	<param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
+        	<param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
+        	<param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
+    		<output name="output_file">
+				<assert_contents>
+            		<has_text text="Contents of File 1" />
+					<has_text text="Contents of File 2" />
+					<has_text text="Contents of File 3" />
+        		</assert_contents>
+			</output>		
+		</test>
+	</tests>
+    <help>
+        .. class:: infomark
+
+        **Purpose**
+
+        To test Galaxy workflow execution and monitoring from Refinery.
+
+        -----
+
+        .. class:: infomark
+
+        **Inputs and outputs**
+
+        This wrapper will accept A Dataset collection list as input and produce a single output file with the concatenated, annotated content of each element in the Dataset Collection.
+
+        *Note:* You must set the "Probability of failure" parameter to a non-zero value
+        for "Write to standard out", "Write to standard error" or "Exit code" to take effect.
+    </help>
+</tool>
diff -r 5b28174e774d -r b87749d7a24c test-data/concat_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concat_output.txt	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,29 @@
+Output file name: "<base_path>"/galaxy/database/files/009/dataset_9980.dat
+
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9977.dat
+
+Output file name: "<base_path>"/galaxy/database/files/009/dataset_9977.dat
+
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9808.dat
+
+Contents of File 3:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9978.dat
+
+Output file name: "<base_path>"/galaxy/database/files/009/dataset_9978.dat
+
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9807.dat
+
+Contents of File 2:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9979.dat
+
+Output file name: "<base_path>"/galaxy/database/files/009/dataset_9979.dat
+
+Input file name: "<base_path>"/galaxy/database/files/009/dataset_9806.dat
+
+Contents of File 1:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
diff -r 5b28174e774d -r b87749d7a24c test-data/file1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/file1.txt	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,4 @@
+Contents of File 1:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
+
diff -r 5b28174e774d -r b87749d7a24c test-data/file2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/file2.txt	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,4 @@
+Contents of File 2:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
+
diff -r 5b28174e774d -r b87749d7a24c test-data/file3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/file3.txt	Thu Feb 22 14:14:03 2018 -0500
@@ -0,0 +1,4 @@
+Contents of File 3:
+TEST TEST TEST TEST
+TEST TEST TEST TEST
+