# HG changeset patch
# User azomics
# Date 1595633089 14400
# Node ID 4f28ee74079b548a86859dba20e0f0ae68f9395e
# Parent  21b2dc3934ede19811d8f9dd18e544c9e5cf17a5
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_pop commit 117c0e4a5c00dfd2e190359badf77d5643fccefa"

diff -r 21b2dc3934ed -r 4f28ee74079b extract_pop/extractpop.py
--- a/extract_pop/extractpop.py	Mon Feb 27 12:50:08 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-
-######################################################################
-#                  Copyright (c) 2016 Northrop Grumman.
-#                          All rights reserved.
-######################################################################
-
-from __future__ import print_function
-import sys
-import pandas as pd
-
-from argparse import ArgumentParser
-
-
-def is_int(s):
-    try:
-        int(s)
-        return True
-    except ValueError:
-        return False
-
-
-def extract_pop(in_file, pop_list, out_file):
-    df = pd.read_table(in_file, dtype={'Population': object})
-    dfout = df.loc[df['Population'].isin(pop_list)]
-    dfout.to_csv(out_file, sep="\t", index=False)
-    return
-
-
-def remove_pop(in_file, pop_list, out_file):
-    df = pd.read_table(in_file, dtype={'Population': object})
-    dfout = df.loc[~df['Population'].isin(pop_list)]
-    dfout.to_csv(out_file, sep="\t", index=False)
-    return
-
-
-if __name__ == "__main__":
-    parser = ArgumentParser(
-             prog="ExtractPop",
-             description="Extract events associated to given population numbers.")
-
-    parser.add_argument(
-            '-i',
-            dest="input_file",
-            required=True,
-            help="File location for the text file.")
-
-    parser.add_argument(
-            '-p',
-            dest="pops",
-            required=True,
-            help="List of populations to extract.")
-
-    parser.add_argument(
-            '-o',
-            dest="output_file",
-            required=True,
-            help="Name of the output file.")
-
-    parser.add_argument(
-            '-m',
-            dest="method",
-            required=True,
-            help="What to do with the populations.")
-
-    args = parser.parse_args()
-
-    # check populations
-    default_values = ["i.e.:2,3,11,25", "default", "Default"]
-    populations = []
-    if args.pops:
-        if args.pops not in default_values:
-            tmp_pops = args.pops.split(",")
-            for popn in tmp_pops:
-                populations.append(popn.strip())
-        else:
-            sys.exit(2)
-    for pops in populations:
-        if not is_int(pops):
-            sys.exit(3)
-    if args.method == "selected":
-        extract_pop(args.input_file, populations, args.output_file)
-    else:
-        remove_pop(args.input_file, populations, args.output_file)
-    sys.exit(0)
diff -r 21b2dc3934ed -r 4f28ee74079b extract_pop/extractpop.xml
--- a/extract_pop/extractpop.xml	Mon Feb 27 12:50:08 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<tool id="extract_pop" name="Extract populations" version="1.0">
-  <description>of interest from FLOCK or Cross Sample output.</description>
-  <requirements>
-    <requirement type="package" version="0.17.1">pandas</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." />
-    <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" />
-  </stdio>
-  <command><![CDATA[
-    python $__tool_directory__/extractpop.py -i "${input}" -o "${output}" -p "${population}" -m "${method}"
-  ]]>
-  </command>
-  <inputs>
-    <param format="flowclr" name="input" type="data" label="Source file"/>
-    <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/>
-  <param name="method" type="select" label="What would you like to do?">
-    <option value="selected">Keep only these populations.</option>
-    <option value="removed">Remove these populations.</option>
-  </param>
-  </inputs>
-  <outputs>
-    <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="input.txt"/>
-      <param name="population" value="2,4"/>
-    <param name="method" value="selected"/>
-      <output name="output" file="output.flowtext"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-   This tool extracts events from given populations from FLOCK or Cross Sample outputs.
-
------
-
-**Input**
-
-FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
-
-**Output**
-
-The input file filtered for selected populations.
-
------
-
-**Example 1**
-
-*Input* - fluorescence intensities per marker and population ID per event::
-
-   Marker1 Marker2 Marker3 Population
-   34      45      12      1
-   33      65      10      5
-   19      62      98      2
-   12      36      58      1
-
-*Populations selected:* 2
-
-*Method:* Keep only the selected populations
-
-*Output* - fluorescence intensities per marker and population ID per event::
-
-   Marker1 Marker2 Marker3 Population
-   19      62      98      2
-
-**Example 2**
-
-*Input* - fluorescence intensities per marker and population ID per event::
-
-   Marker1 Marker2 Marker3 Population
-   34      45      12      1
-   33      65      10      5
-   19      62      98      2
-   12      36      58      1
-
- *Populations selected:* 2
-
- *Method:* Remove the selected populations
-
- *Output* - fluorescence intensities per marker and population ID per event::
-
-    Marker1 Marker2 Marker3 Population
-    34      45      12      1
-    33      65      10      5
-    12      36      58      1
-
-  ]]>
-  </help>
-</tool>
diff -r 21b2dc3934ed -r 4f28ee74079b extract_pop/test-data/input.txt
--- a/extract_pop/test-data/input.txt	Mon Feb 27 12:50:08 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4	Population
-449	157	551	129	169	292	1
-894	1023	199	277	320	227	4
-262	73	437	69	0	146	1
-340	115	509	268	0	74	2
-316	76	50	0	60	129	5
-394	144	83	138	335	194	3
-383	139	499	0	0	224	6
-800	1023	239	284	288	280	2
-388	97	534	111	83	177	4
diff -r 21b2dc3934ed -r 4f28ee74079b extract_pop/test-data/output.flowtext
--- a/extract_pop/test-data/output.flowtext	Mon Feb 27 12:50:08 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4	Population
-894	1023	199	277	320	227	4
-340	115	509	268	0	74	2
-800	1023	239	284	288	280	2
-388	97	534	111	83	177	4
diff -r 21b2dc3934ed -r 4f28ee74079b extractpop.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractpop.py	Fri Jul 24 19:24:49 2020 -0400
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+
+from __future__ import print_function
+import sys
+import pandas as pd
+
+from argparse import ArgumentParser
+
+
+def is_int(s):
+    try:
+        int(s)
+        return True
+    except ValueError:
+        return False
+
+
+def extract_pop(in_file, pop_list, out_file):
+    df = pd.read_table(in_file, dtype={'Population': object})
+    dfout = df.loc[df['Population'].isin(pop_list)]
+    dfout.to_csv(out_file, sep="\t", index=False)
+    return
+
+
+def remove_pop(in_file, pop_list, out_file):
+    df = pd.read_table(in_file, dtype={'Population': object})
+    dfout = df.loc[~df['Population'].isin(pop_list)]
+    dfout.to_csv(out_file, sep="\t", index=False)
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="ExtractPop",
+             description="Extract events associated to given population numbers.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_file",
+            required=True,
+            help="File location for the text file.")
+
+    parser.add_argument(
+            '-p',
+            dest="pops",
+            required=True,
+            help="List of populations to extract.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    parser.add_argument(
+            '-m',
+            dest="method",
+            required=True,
+            help="What to do with the populations.")
+
+    args = parser.parse_args()
+
+    # check populations
+    default_values = ["i.e.:2,3,11,25", "default", "Default"]
+    populations = []
+    if args.pops:
+        if args.pops not in default_values:
+            tmp_pops = args.pops.split(",")
+            for popn in tmp_pops:
+                populations.append(popn.strip())
+        else:
+            sys.exit(2)
+    for pops in populations:
+        if not is_int(pops):
+            sys.exit(3)
+    if args.method == "selected":
+        extract_pop(args.input_file, populations, args.output_file)
+    else:
+        remove_pop(args.input_file, populations, args.output_file)
diff -r 21b2dc3934ed -r 4f28ee74079b extractpop.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractpop.xml	Fri Jul 24 19:24:49 2020 -0400
@@ -0,0 +1,92 @@
+<tool id="extract_pop" name="Extract populations" version="1.0+galaxy0" profile="18.01">
+  <description>of interest from FLOCK or Cross Sample output</description>
+  <requirements>
+    <requirement type="package" version="1.0.5">pandas</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1"/>
+    <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." />
+    <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" />
+    <exit_code range="4:"/>
+  </stdio>
+  <command><![CDATA[
+    python '$__tool_directory__/extractpop.py' -i '${input}' -o '${output}' -p '${population}' -m '${method}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowclr" name="input" type="data" label="Source file"/>
+    <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/>
+    <param name="method" type="select" label="What would you like to do?">
+      <option value="selected">Keep only these populations.</option>
+      <option value="removed">Remove these populations.</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.txt"/>
+      <param name="population" value="2,4"/>
+      <param name="method" value="selected"/>
+      <output name="output" file="output.flowtext"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool extracts events from given populations from FLOCK or Cross Sample outputs.
+
+-----
+
+**Input**
+
+FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
+
+**Output**
+
+The input file filtered for selected populations.
+
+-----
+
+**Example 1**
+
+*Input* - fluorescence intensities per marker and population ID per event::
+
+   Marker1 Marker2 Marker3 Population
+   34      45      12      1
+   33      65      10      5
+   19      62      98      2
+   12      36      58      1
+
+*Populations selected:* 2
+
+*Method:* Keep only the selected populations
+
+*Output* - fluorescence intensities per marker and population ID per event::
+
+   Marker1 Marker2 Marker3 Population
+   19      62      98      2
+
+**Example 2**
+
+*Input* - fluorescence intensities per marker and population ID per event::
+
+   Marker1 Marker2 Marker3 Population
+   34      45      12      1
+   33      65      10      5
+   19      62      98      2
+   12      36      58      1
+
+ *Populations selected:* 2
+
+ *Method:* Remove the selected populations
+
+ *Output* - fluorescence intensities per marker and population ID per event::
+
+    Marker1 Marker2 Marker3 Population
+    34      45      12      1
+    33      65      10      5
+    12      36      58      1
+
+  ]]>
+  </help>
+</tool>
diff -r 21b2dc3934ed -r 4f28ee74079b test-data/input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.txt	Fri Jul 24 19:24:49 2020 -0400
@@ -0,0 +1,10 @@
+Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4	Population
+449	157	551	129	169	292	1
+894	1023	199	277	320	227	4
+262	73	437	69	0	146	1
+340	115	509	268	0	74	2
+316	76	50	0	60	129	5
+394	144	83	138	335	194	3
+383	139	499	0	0	224	6
+800	1023	239	284	288	280	2
+388	97	534	111	83	177	4
diff -r 21b2dc3934ed -r 4f28ee74079b test-data/output.flowtext
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.flowtext	Fri Jul 24 19:24:49 2020 -0400
@@ -0,0 +1,5 @@
+Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4	Population
+894	1023	199	277	320	227	4
+340	115	509	268	0	74	2
+800	1023	239	284	288	280	2
+388	97	534	111	83	177	4