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1 <tool id="collapse_populations" name="Collapse populations" version="1.0">
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2 <description>from FLOCK or Cross Sample analysis.</description>
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3 <requirements>
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4 <requirement type="package" version="0.17.1">pandas</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="2" level="warning" description="The color code only allows populations between 1 and 40." />
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8 <exit_code range="3" level="warning" description="The same population to collapse into is being used several times." />
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9 <exit_code range="4" level="fatal" description="Please provide a comma separated list of populations to collapse." />
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10 <exit_code range="5" level="warning" description="The color code only allows populations between 1 and 40, and the same population to collapse into is being used several times." />
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11 <exit_code range="6" level="fatal" description="The populations must be integers (i.e,: 1,2,4.)" />
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12 <exit_code range="7" level="fatal" description="The same population is being collapsed into 2 different populations." />
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13 </stdio>
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14 <command><![CDATA[
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15 python $__tool_directory__/collapse_pops.py -o "${output}" -i "${input}" -p "${population}" -c "${collapse}"
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16 #for $repeats in $repeat_option
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17 -p "${repeats.population}"
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18 -c "${repeats.collapse}"
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19 #end for
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param format="flowclr" name="input" type="data" label="Source file"/>
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24 <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
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25 <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
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26 <repeat name="repeat_option" title="more populations to manipulate:">
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27 <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
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28 <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
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29 </repeat>
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30 </inputs>
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31 <outputs>
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32 <data format="flowclr" name="output" label="${input.name} with renamed populations"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="input.flowclr"/>
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37 <param name="population" value="2,3,4"/>
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38 <param name="collapse" value="1"/>
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39 <output name="output" file="output.flowclr"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 This tool collapses several populations into one.
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44
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45 -----
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46
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47 .. class:: warningmark
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48
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49 Tip: You can use this tool to assign specific colors to your populations in the FLOCK and Cross Sample overview tools. The color scheme we use is the following:
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50
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51 .. image:: static/images/liz_colorcode.png
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52
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53 -----
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54
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55 **Input**
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56
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57 FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
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58
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59 **Output**
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60
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61 The input file with selected populations replaced by the indicated population.
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62
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63 -----
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64
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65 **Example**
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66
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67 *Input* - fluorescence intensities per marker and population ID per event::
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68
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69 Marker1 Marker2 Marker3 Population
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70 34 45 12 1
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71 33 65 10 5
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72 19 62 98 2
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73 12 36 58 1
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74
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75 *Populations selected:* 2, 5
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76
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77 *Collapse into population:* 3
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78
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79 *Output* - fluorescence intensities per marker and population ID per event::
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80
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81 Marker1 Marker2 Marker3 Population
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82 34 45 12 1
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83 33 65 10 3
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84 19 62 98 3
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85 12 36 58 1
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86
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87 ]]>
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88 </help>
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89 </tool>
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