Mercurial > repos > immport-devteam > cross_sample
annotate runCrossSample.xml @ 4:e80b0f62ffb3 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
| author | azomics |
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| date | Wed, 29 Jul 2020 13:32:17 -0400 |
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| rev | line source |
|---|---|
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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1 <tool id="run_cross_sample" name="Run Cross Sample" version="1.1+galaxy0" profile="18.01"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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2 <description>using a Flow file that was run using FLOCK</description> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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3 <requirements> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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4 <requirement type="package" version="1.5.1">scipy</requirement> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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5 <requirement type="package" version="1.0.5">pandas</requirement> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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6 <requirement type="package" version="1.0">flock</requirement> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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7 </requirements> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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8 <stdio> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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9 <exit_code range="1" level="fatal"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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10 <exit_code range="2" level="fatal" description="Columns inconsistencies between files and centroids file. See stderr for more details." /> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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11 <exit_code range="3:" level="fatal"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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12 </stdio> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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13 <command><![CDATA[ |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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14 python '$__tool_directory__/runCrossSample.py' -m '${centroid}' -s '${stats}' -S '${mfistats}' -a '${allstats}' -M '${mfi}' -o crossSampleOutputs |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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15 #for $f in $input |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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16 -i $f |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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17 -n '${f.name}' |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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18 #end for |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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19 |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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20 ]]> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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21 </command> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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22 <inputs> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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23 <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Flowtext files Collection"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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24 <param format="flowmfi" name="centroid" type="data" label="Centroid file"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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25 <param name="mfi" type="select" label="Calculate centroids using:"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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26 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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27 <option value="mdfi">Median Fluorescence Intensity</option> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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28 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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29 </param> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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30 </inputs> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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31 <outputs> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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32 <collection type="list" label="CrossSample on ${input.name}" name="output"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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33 <discover_datasets pattern="(?P<name>.*)" directory="crossSampleOutputs" format="flowclr" /> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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34 </collection> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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35 <data format="flowstat1" name="stats" label="Population distribution after CrossSample on ${input.name} using ${mfi}"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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36 <data format="flowstat2" name="mfistats" label="${mfi} centroids of CrossSample on ${input.name} using ${mfi}"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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37 <data format="flowstat3" name="allstats" label="${mfi} descriptive stats of CrossSample on ${input.name} using ${mfi}"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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38 </outputs> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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39 <tests> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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40 <test> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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41 <param name="input"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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42 <collection type="list"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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43 <element name="input1" value="input1.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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44 <element name="input2" value="input2.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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45 <element name="input3" value="input3.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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46 </collection> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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47 </param> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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48 <param name="centroid" value="mfi.flowmfi"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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49 <param name="mfi" value="mfi"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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50 <output name="stats" file="out1.flowstat1" lines_diff="6"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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51 <output name="allstats" file="out1.flowstat3"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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52 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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53 <output_collection name="output" count="3"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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54 <element name="input1.flowtext.flowclr" file="run1/input1.flowtext.flowclr" compare="sim_size"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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55 <element name="input2.flowtext.flowclr" file="run1/input2.flowtext.flowclr" compare="sim_size"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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56 <element name="input3.flowtext.flowclr" file="run1/input3.flowtext.flowclr" compare="sim_size"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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57 </output_collection> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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58 </test> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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59 <test> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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60 <param name="input"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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61 <collection type="list"> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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62 <element name="input1" value="input1.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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63 <element name="input2" value="input2.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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64 <element name="input3" value="input3.flowtext"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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65 </collection> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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66 </param> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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67 <param name="centroid" value="gmfi.flowmfi"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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68 <param name="mfi" value="gmfi"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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69 <output name="stats" file="out2.flowstat1" lines_diff="6"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
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70 <output name="allstats" file="out2.flowstat3"/> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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71 <output name="mfistats" file="out2.flowstat2" compare="sim_size"/> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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72 <output_collection name="output" type="list" count="3"> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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73 <element name="input1.flowtext.flowclr" file="run2/input1.flowtext.flowclr"/> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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74 <element name="input2.flowtext.flowclr" file="run2/input2.flowtext.flowclr"/> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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75 <element name="input3.flowtext.flowclr" file="run2/input3.flowtext.flowclr"/> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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76 </output_collection> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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77 </test> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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78 </tests> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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79 <help><![CDATA[ |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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80 This tool runs CrossSample using the MFI from FLOCK and text-converted FCS files. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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81 ----- |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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82 **Input** |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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83 This tool compares text-converted FCS files from a data collection to the MFI generated by a FLOCK run. The same data collection merged and run with FLOCK should be used to ensure consistency in the attribution of events to populations. |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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84 .. class:: infomark |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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85 The option chosen for the centroids (mean, median or geometric mean) should be the same as used to run FLOCK. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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86 **Output** |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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87 Each event within each file of a dataset collection is attributed to a population depending on its intensity profile. |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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88 A table of the population composition of each file is generated as well as MFI and population descriptive statistics. |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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89 .. class:: infomark |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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90 Tip: If headers in each text-converted FCS file do not match those in the centroid file, the program will not run. Edit the input file using the Remove, rearrange and/or rename columns tool in the Flow Text File Tools section prior to Cross Sample analysis. |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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91 ----- |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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92 **Example** |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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93 *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/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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94 Marker1 Marker2 Marker3 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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95 33 47 11 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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96 31 64 11 ... |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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97 21 62 99 ... |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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98 14 34 60 ... |
|
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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99 ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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100 *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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101 Population Marker1 Marker2 Marker3 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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102 1 38 49 10 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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103 2 21 63 100 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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104 3 31 52 45 ... |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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105 4 11 78 25 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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106 ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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107 *Output* for each text file - 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/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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108 Marker1 Marker2 Marker3 ... Population |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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109 33 47 11 ... 1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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110 31 64 11 ... 6 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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111 21 62 99 ... 2 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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112 14 34 60 ... 7 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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113 ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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114 *Summary table* - distribution of events in each population in each file:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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115 Filename SampleName Pop1 Pop2 Pop3 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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116 File1 Biosample1 0.1 0.25 0.14 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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117 File2 Biosample2 0.02 0.1 0.17 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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118 File3 Biosample3 0.4 0.05 0.21 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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119 File4 Biosample4 0.05 0.3 0.08 ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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120 *Centroid MFI Summary table* - for each file, mean, median or geometric mean fluorescence intensities per marker per population:: |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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121 Marker1 Marker2 Marker3 ... Population Percentage SampleName |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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122 154 885 24 ... 1 0.2 Biosample1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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123 458 74 574 ... 2 0.3 Biosample1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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124 3 210 86 ... 3 0.05 Biosample1 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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125 ... ... ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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126 140 921 19 ... 1 0.1 Biosample2 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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127 428 79 508 ... 2 0.25 Biosample2 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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128 9 225 90 ... 3 0.3 Biosample2 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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129 ... ... ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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130 *MFI Descriptive Statistics table* - for the set of files, mean, median and standard deviation of each centroid per marker per population, as well as mean, median and standard deviation of the population's proportion:: |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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131 Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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132 1 94.65 90.86 25.8 ... 1.84 0.55 2.48 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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133 2 132.18 131.58 5.02 ... 9.89 9.76 0.33 |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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134 3 71.8 69.68 10.53 ... 3.02 1.49 3.45 |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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135 4 84.85 84.85 nan ... 8.52 8.52 nan |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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136 5 161.82 132.77 61.29 ... 0.95 0.37 1.06 |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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137 ... ... ... ... ... ... ... ... |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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138 ]]> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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139 </help> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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140 <citations> |
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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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141 <citation type="doi">10.1002/cyto.b.20554</citation> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
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142 <citation type="doi">10.3389/fimmu.2012.00302</citation> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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143 <citation type="doi">10.1371/journal.pone.0038408</citation> |
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e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
diff
changeset
|
144 <citation type="doi">10.1371/journal.ppat.1003076</citation> |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
diff
changeset
|
145 <citation type="doi">10.1016/j.clim.2012.12.003</citation> |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
diff
changeset
|
146 <citation type="doi">10.1038/srep02327</citation> |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
diff
changeset
|
147 </citations> |
|
e80b0f62ffb3
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
azomics
parents:
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148 </tool> |