Mercurial > repos > immport-devteam > run_flock
annotate runFlockMFI.xml @ 2:b6b4d08b6858 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
author | azomics |
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date | Fri, 17 Jul 2020 09:06:54 -0400 |
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2
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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1 <tool id="run_flock" name="Run FLOCK" version="1.2+galaxy0" profile="18.01"> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
2 <description>using a FCS file that was converted/transformed to a text file</description> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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3 <requirements> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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4 <requirement type="package" version="1.5.1">scipy</requirement> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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5 <requirement type="package" version="1.0.5">pandas</requirement> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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6 <requirement type="package" version="1.0">flock</requirement> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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7 </requirements> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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8 <stdio> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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9 <exit_code range="1:" /> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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10 </stdio> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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11 <command><![CDATA[ |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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12 python3 '$__tool_directory__/runFlockMFI.py' -i '${input}' -m '${method}' -o '${output}' -c '${centroid}' -M '${mfi}' -p '${profile}' |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
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13 #if $bins |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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14 -b $bins |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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15 #end if |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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16 #if $density |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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17 -d $density |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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18 #end if |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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19 ]]> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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20 </command> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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21 <inputs> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
22 <param format="flowtext" name="input" type="data" label="Source file"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
23 <param name="method" type="select" label="Method"> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
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changeset
|
24 <option value="flock1" selected="true">Flock Version 1</option> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
25 <option value="flock2">Flock Version 2</option> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
26 </param> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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27 <param name="bins" type="integer" min="6" max="30" optional="true" value="" label="bins (6-30)"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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28 <param name="density" type="integer" min="2" max="100" optional="true" value="" label="density (2-100)"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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29 <param name="mfi" type="select" label="Calculate centroids using:"> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
30 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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31 <option value="mdfi">Median Fluorescence Intensity</option> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
32 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
33 </param> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
34 </inputs> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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35 <outputs> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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36 <data format="flowclr" name="output" label="${method} with ${mfi} on ${input.name}"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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37 <data format="flowmfi" name="centroid" label="${mfi} centroids from ${method} on ${input.name}"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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38 <data format="flowscore" name="profile" label="Population score profiles from ${method} on ${input.name}"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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39 </outputs> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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40 <tests> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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41 <test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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42 <param name="input" value="input.flowtext"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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43 <param name="method" value="flock1"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
44 <param name="bins" value=""/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
45 <param name="density" value=""/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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46 <param name="mfi" value="mfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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47 <output name="output" file="out1.flowclr"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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48 <output name="centroid" file="mfi.flowmfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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49 <output name="profile" file="out1.flowscore"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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50 </test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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51 <test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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52 <param name="input" value="input.flowtext"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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53 <param name="method" value="flock2"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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54 <param name="bins" value=""/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
|
55 <param name="density" value=""/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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56 <param name="mfi" value="mfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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57 <output name="output" file="out2.flowclr"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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58 <output name="centroid" file="mfi2.flowmfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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59 <output name="profile" file="out2.flowscore"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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60 </test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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61 <test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
changeset
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62 <param name="input" value="input.flowtext"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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63 <param name="method" value="flock1"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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64 <param name="bins" value="7"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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65 <param name="density" value="3"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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66 <param name="mfi" value="mfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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67 <output name="output" file="out3.flowclr"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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68 <output name="centroid" file="mfi3.flowmfi"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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69 <output name="profile" file="out3.flowscore"/> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
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70 </test> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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71 </tests> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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72 <help><![CDATA[ |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
diff
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73 This tool runs FLOCK using a FCS file that was converted to a text file. |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
parents:
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74 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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75 ----- |
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76 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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77 .. image:: ./static/images/flowtools/flock_logo.png |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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78 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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79 FLOCK (FLOw Clustering without K) is a computational approach to flow cytometry analysis which: |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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80 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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81 1. Computationally determines the number of unique populations in high dimensional flow data using a rapid binning approach |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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82 2. Can handle non-spherical hyper-shapes |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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83 3. Maps populations across independent samples |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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84 4. Calculates many useful summary statistics |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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85 5. Finds the most informative parameters |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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86 6. Reduces subjective factors in manual gating |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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87 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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88 .. class:: warningmark |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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89 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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90 This tool is not intended to analyze CyTOF data as is. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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91 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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92 ----- |
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93 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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94 **Input** |
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95 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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96 FLOCK requires a text file, generated from a FCS file, as input. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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97 In order to define the populations in a given dataset collection for a given set of markers, run FLOCK on a super-set of FCS file. Use the Downsample and merge tool to concatenate and/or downsample datasets, and remove, edit or rearrange markers before running FLOCK on your favorite set of markers. |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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98 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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99 .. class:: infomark |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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100 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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101 Tip: Make sure to keep only columns containing data from markers. |
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102 |
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103 **Output** |
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104 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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105 *FLOCK* |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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106 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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107 FLOCK attributes each event to a population and generates a text file. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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108 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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109 *Centroids* |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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110 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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111 The centroid file is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK, as determined by the user. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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112 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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113 *Population scores* |
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114 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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115 This output is a table containing marker scores for each population. The score value is a number indicating the degree to which this population expresses each marker, as follows: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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116 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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117 - 1 implies negative expression |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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118 - 2 implies low expression |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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119 - 3 implies positive expression |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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120 - 4 implies highly positive expression |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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121 |
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122 ----- |
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123 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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124 **Example** |
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125 |
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126 *Input* - fluorescence intensities per marker per event:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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127 |
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128 Marker1 Marker2 Marker3 ... |
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129 34 45 12 ... |
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130 33 65 10 ... |
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131 19 62 98 ... |
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132 12 36 58 ... |
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133 ... ... ... ... |
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134 |
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135 *FLOCK Output* - fluorescence intensities per marker and population ID per event:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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136 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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137 Marker1 Marker2 Marker3 ... Population |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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138 34 45 12 ... 1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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139 33 65 10 ... 5 |
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140 19 62 98 ... 2 |
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141 12 36 58 ... 1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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142 ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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143 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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144 *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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145 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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146 Population Marker1 Marker2 Marker3 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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147 1 38 49 10 ... |
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148 2 21 63 100 ... |
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149 3 31 52 45 ... |
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150 4 11 78 25 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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151 ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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152 |
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153 *Population profile file*:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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154 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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155 Population_ID Marker1 Marker2 Marker3 ... Count Percentage |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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156 1 1 3 2 ... 3885 6.44 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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157 2 1 3 4 ... 2774 4.62 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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158 3 2 2 3 ... 2151 3.59 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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159 4 1 3 2 ... 1207 2.01 |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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160 ... ... ... ... ... ... ... |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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161 ]]> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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162 </help> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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163 <citations> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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164 <citation type="doi">10.1002/cyto.b.20554</citation> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
azomics
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165 </citations> |
b6b4d08b6858
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
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166 </tool> |