diff extractpop.xml @ 1:4f28ee74079b draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_pop commit 117c0e4a5c00dfd2e190359badf77d5643fccefa"

--- /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>