Mercurial > repos > azomics > edit_fcs_markers

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
author azomics
date Mon, 22 Jun 2020 20:07:30 -0400
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02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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1 <tool id="edit_fcs_markers" name="Edit markers or channels" version="1.0">
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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2 <description>in FCS files</description>
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3 <requirements>
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4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="10" level="fatal" description="Please provide a valid FCS file." />
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8 <exit_code range="11" level="fatal" description="Please provide a comma separated list of integers for markers/channels you want to rename." />
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9 <exit_code range="12" level="fatal" description="Please provide a comma separated list of names for markers/channels you want to rename." />
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10 <exit_code range="13" level="fatal" description="List of marker indices and marker names must match. For instance, indices 1,3,4 and Marker4,Marker6,Marker8." />
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11 <exit_code range="14" level="fatal" description="Provided indices are out of range in the FCS file given as input." />
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12 </stdio>
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13 <command><![CDATA[
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14 Rscript --slave --vanilla '$__tool_directory__/editFCSmarkers.R' '${input}' '${output_file}' '${outformat}' '${report}' '${columns}' '${colnames}' '${corm}'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="fcs" name="input" type="data" label="Text file"/>
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19 <param name="columns" type="text" label="Channels or markers to modify" help="These are comma separated (ie.: 'ColX,ColY'). The column names provided need to exist in the flowFrame / FCS file provided as input. If you're not sure, check your markers with the list of markers tool in the FCS File Tools section."/>
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20 <param name="colnames" type="text" label="New column headings" help="New names for the column headers, a comma separated list of the same lenght as 'Channels or markers to modify' (i.e.: 'Marker1,Marker6,Marker4'). Check below for more details.">
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21 </param>
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22 <param name="corm" type="select" label="Modify Channels or Markers?" help="If you are not sure which to modify, check with the list of marker tools in the FCS File Tools section.">
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23 <option value="M">Markers</option>
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24 <option value="C">Channels</option>
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25 </param>
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26 <param name="outformat" type="select" label="Output Format">
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27 <option value="flowFrame">R Data, flowFrame</option>
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28 <option value="FCS">FCS 3.0</option>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="txt" name="report" label="Editing Report of FCS markers from ${input.name}"/>
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33 <data format="flowframe" name="output_file" label="Edited FCS from ${input.name} in ${outformat}">
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34 <change_format>
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35 <when input="outformat" value="FCS" format="fcs" />
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36 </change_format>
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37 </data>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="input.fcs"/>
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42 <param name="columns" value="Forward Scatter,Side Scatter,APC CD45RA"/>
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43 <param name="colnames" value="m1,m2,m3"/>
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44 <param name="corm" value="M"/>
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45 <param name="outformat" value="flowFrame"/>
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46 <output name="report" value="report1.txt"/>
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47 <output name="output_file" file="output.flowframe" compare="sim_size" delta="500000"/>
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48 </test>
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49 <test>
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50 <param name="input" value="input.fcs"/>
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51 <param name="columns" value="FSC-H,SSC-H,FL4-H"/>
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52 <param name="colnames" value="m1,m2,m3"/>
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53 <param name="corm" value="C"/>
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54 <param name="outformat" value="FCS"/>
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55 <output name="report" value="report2.txt"/>
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56 <output name="output_file" file="output.fcs" compare="sim_size" delta="500000"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 This tool enables editing FCS markers or channels.
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61
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62 -----
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63
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64 **Input files**
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65
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66 This tool requires FCS files as input.
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67
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68 **Column names**
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69
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70 Please indicate the names of the markers / channels to edit (comma-separated list).
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71
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72 .. class:: infomark
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73
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74 Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
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75
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76 - Get list of markers and channels in FCS files.
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77
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78 **Column names**
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79
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80 Please indicate the new marker or channel names in the order in which they should appear in the output file (comma-separated list). The number of names should match the number of indices.
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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81
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82 **Output file**
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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83
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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84 The output contains the input data with new marker or channel names. Output can be provided in FCS format or in a RData object containing a flowFrame.
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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85
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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86 -----
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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87
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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88 **Examples**
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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89
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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90 **Input file**::
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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91
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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92 Marker1 Marker2 Marker3 Marker4 Marker5
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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93 4 45 123 1956 62534
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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94 3 65 104 1254 36576
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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95 7 26 767 4124 42235
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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96 4 56 323 7623 74634
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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97 5 83 532 6256 34763
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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98 4 15 877 9312 21265
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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99 ... ... ... ... ...
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100
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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101 *Example 1*
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102
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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103 - Indices: Marker1,Marker3,Marker5
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104 - Column names: Marker7,Marker8,Marker9
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105
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106 *Output1*::
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107
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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108 Marker7 Marker2 Marker8 Marker4 Marker9
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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109 4 45 123 1956 62534
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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110 3 65 104 1254 36576
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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111 7 26 767 4124 42235
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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112 4 56 323 7623 74634
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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113 5 83 532 6256 34763
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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114 4 15 877 9312 21265
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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115 ... ... ... ... ...
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116
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117 ]]>
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118 </help>
02b2412598b6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
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119 </tool>