Mercurial > repos > azomics > ggcyto_1d_density_plots

annotate FCS1Dplotggcyto.xml @ 0:b73fc4860906 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
author azomics
date Mon, 22 Jun 2020 17:53:11 -0400
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b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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1 <tool id="ggcyto_1d_density_plots" name="Generate 1D density plots" version="1.1+galaxy0">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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2 <description>for FCS file</description>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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3 <requirements>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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4 <requirement type="package" version="1.14.0">bioconductor-ggcyto</requirement>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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5 <!-- to fix https://github.com/RGLab/ggcyto/issues/64 and not able to install ggcyto 1.16.0-->
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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6 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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7 </requirements>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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8 <stdio>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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9 <exit_code range="1:" />
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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10 </stdio>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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11 <command><![CDATA[
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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12 Rscript $__tool_directory__/FCS1Dplotggcyto.R '${input}' '${output}' $outformat '${transform.trans_method}'
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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13 #if $transform.trans_method == "arcsinh"
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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14 $transform.scaling_factor
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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15 #else if $transform.trans_method == "logicle"
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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16 $transform.w $transform.t $transform.m
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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17 #end if
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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18 ]]>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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19 </command>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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20 <inputs>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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21 <param format="fcs" name="input" type="data" label="FCS file"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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22 <conditional name="transform">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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23 <param name="trans_method" type="select" label="Apply transformation to plot:" help="by default, no transformation">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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24 <option value="None">no transformation please.</option>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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25 <option value="logicle">logicle</option>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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26 <option value="arcsinh">arcsinh</option>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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27 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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28 <when value="arcsinh">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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29 <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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30 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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31 </when>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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32 <when value="logicle">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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33 <param name="w" type="float" value="0.5" label="Linearization width w for logicle transform:" help="w should be positive and determines the slope of transformation at zero. The default value is 0.5.">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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34 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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35 <param name="t" type="integer" value="262144" label="Top of the scale data value t for logicle transform:" help=" t should be greater than zero. Recommended values are 10000 for common 4 decade data or 262144 for a 18 bit data range. The default value is 262144.">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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36 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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37 <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 .">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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38 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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39 </when>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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40 </conditional>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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41 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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42 <option value="PNG">PNG</option>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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43 <option value="PDF">PDF</option>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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44 </param>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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45 </inputs>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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46 <outputs>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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47 <data format="png" name="output" label="1D Density Plots for ${input.name} with ${transform.trans_method} in ${outformat}">
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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48 <change_format>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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49 <when input="outformat" value="PDF" format="pdf" />
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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50 </change_format>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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51 </data>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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52 </outputs>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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53 <tests>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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54 <test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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55 <param name="input" value="testfcs1.fcs"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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56 <param name="outformat" value="PDF"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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57 <param name="trans_method" value="None"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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58 <output name="output" file="graph.pdf" compare="sim_size"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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59 </test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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60 <test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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61 <param name="input" value="testfcs1.fcs"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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62 <param name="outformat" value="PNG"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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63 <param name="trans_method" value="logicle"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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64 <param name="w" value="0.4"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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65 <param name="m" value="4.5"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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66 <param name="t" value="10000"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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67 <output name="output" file="graph1.png" compare="sim_size"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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68 </test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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69 <test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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70 <param name="input" value="testfcs1.fcs"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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71 <param name="outformat" value="PNG"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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72 <param name="trans_method" value="arcsinh"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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73 <param name="scaling_factor" value="150"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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74 <output name="output" file="graph2.png" compare="sim_size"/>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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75 </test>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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76 </tests>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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77 <help><![CDATA[
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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78 Scatterplots of fcs sample
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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79 -------------------
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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80
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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81 This tool allows generation of density scatter plots using ggcyto.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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82
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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83 **Input files**
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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84
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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85 This tool takes valid FCS files as input.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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86
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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87 **Output files**
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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88
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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89 This tool generates a series of 1D density plot using ggcyto and produces a png file. A pdf file can optionally be generated.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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90
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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91 class:: warningmark
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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92
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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93 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.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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94
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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95 -----
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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96
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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97 **Transformation**
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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98
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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99 This tools currently supports 2 transformation algorithms: arcsinh and logicle, implemented using flowCore. Transformation applied are color-coded: black is no transformation, blue is arcinsh, and green is logicle.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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100
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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101 -----
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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102
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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103 **Example**
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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104
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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105 *Output*:
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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106
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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107 .. image:: ./static/images/flowtools/testoutputggcyto.png
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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108
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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109 -----
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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110
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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111 **ggcyto reference**
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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112 Jiang M (2015). ggcyto: Visualize Cytometry data with ggplot. R package version 1.4.0, https://github.com/RGLab/ggcyto/issues.
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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113
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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114 ]]>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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115 </help>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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116 <citations>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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117 <citation type="doi">10.1186/1471-2105-10-106</citation>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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118 </citations>
b73fc4860906 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
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119 </tool>