Mercurial > repos > immport-devteam > fcs_scatterplot
annotate getDensityPlots.xml @ 1:413f3e610295 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
| author | azomics |
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| date | Thu, 16 Jul 2020 08:00:52 -0400 |
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| rev | line source |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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1 <tool id="gen_density_plots" name="Generate scatter plots" version="1.0+galaxy0"> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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2 <description>for any given markers in FCS file</description> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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3 <requirements> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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4 <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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5 </requirements> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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6 <stdio> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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7 <exit_code range="1:9" level="fatal" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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8 <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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9 <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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10 <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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11 <exit_code range="13:" level="fatal" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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12 </stdio> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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13 <command><![CDATA[ |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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14 Rscript --slave --vanilla '$__tool_directory__/getDensityPlots.R' '${input}' '${channels}' '${output}' '${outformat}' |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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15 ]]> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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16 </command> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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17 <inputs> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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18 <param format="fcs" name="input" type="data" label="FCS file"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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19 <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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20 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load."> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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21 <option value="PNG">PNG</option> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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22 <option value="PDF">PDF</option> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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23 </param> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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24 </inputs> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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25 <outputs> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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26 <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}"> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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27 <change_format> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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28 <when input="outformat" value="PDF" format="pdf" /> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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29 </change_format> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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30 </data> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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31 </outputs> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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32 <tests> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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33 <test> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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34 <param name="input" value="testfcs1.fcs"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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35 <param name="channels" value="1,3"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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36 <param name="outformat" value="PDF"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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37 <output name="output" file="graph.pdf" compare="sim_size" delta="1000000"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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38 </test> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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39 <test> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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40 <param name="input" value="testfcs1.fcs"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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41 <param name="channels" value="i.e.:1,3,4"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
parents:
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42 <param name="outformat" value="PNG"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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43 <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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44 </test> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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45 </tests> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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46 <help><![CDATA[ |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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47 This tool allows generation of density scatter plots using flowDensity. |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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48 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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49 ----- |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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50 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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51 **Input files** |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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52 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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53 This tool takes valid FCS files as input. |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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54 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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55 **Output files** |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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56 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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57 This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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58 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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59 class:: warningmark |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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60 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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61 PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally. |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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62 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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63 ----- |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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64 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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65 **Example** |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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66 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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67 *Output*: |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
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68 |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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69 .. image:: ./static/images/flowtools/densityplots.png |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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70 ]]> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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71 </help> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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72 <citations> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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73 <citation type="doi">10.1093/bioinformatics/btu677</citation> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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74 <citation type="doi">10.1186/1471-2105-10-106</citation> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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75 </citations> |
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413f3e610295
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
azomics
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76 </tool> |