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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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1 <tool id="edit_fcs_markers" name="Edit markers or channels" version="1.0">
2 <description>in FCS files</description>
3 <requirements>
4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="10" level="fatal" description="Please provide a valid FCS file." />
8 <exit_code range="11" level="fatal" description="Please provide a comma separated list of integers for markers/channels you want to rename." />
9 <exit_code range="12" level="fatal" description="Please provide a comma separated list of names for markers/channels you want to rename." />
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." />
11 <exit_code range="14" level="fatal" description="Provided indices are out of range in the FCS file given as input." />
12 </stdio>
13 <command><![CDATA[
14 Rscript --slave --vanilla '$__tool_directory__/editFCSmarkers.R' '${input}' '${output_file}' '${outformat}' '${report}' '${columns}' '${colnames}' '${corm}'
15 ]]>
16 </command>
17 <inputs>
18 <param format="fcs" name="input" type="data" label="Text file"/>
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."/>
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.">
21 </param>
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.">
23 <option value="M">Markers</option>
24 <option value="C">Channels</option>
25 </param>
26 <param name="outformat" type="select" label="Output Format">
27 <option value="flowFrame">R Data, flowFrame</option>
28 <option value="FCS">FCS 3.0</option>
29 </param>
30 </inputs>
31 <outputs>
32 <data format="txt" name="report" label="Editing Report of FCS markers from ${input.name}"/>
33 <data format="flowframe" name="output_file" label="Edited FCS from ${input.name} in ${outformat}">
34 <change_format>
35 <when input="outformat" value="FCS" format="fcs" />
36 </change_format>
37 </data>
38 </outputs>
39 <tests>
40 <test>
41 <param name="input" value="input.fcs"/>
42 <param name="columns" value="Forward Scatter,Side Scatter,APC CD45RA"/>
43 <param name="colnames" value="m1,m2,m3"/>
44 <param name="corm" value="M"/>
45 <param name="outformat" value="flowFrame"/>
46 <output name="report" value="report1.txt"/>
47 <output name="output_file" file="output.flowframe" compare="sim_size" delta="500000"/>
48 </test>
49 <test>
50 <param name="input" value="input.fcs"/>
51 <param name="columns" value="FSC-H,SSC-H,FL4-H"/>
52 <param name="colnames" value="m1,m2,m3"/>
53 <param name="corm" value="C"/>
54 <param name="outformat" value="FCS"/>
55 <output name="report" value="report2.txt"/>
56 <output name="output_file" file="output.fcs" compare="sim_size" delta="500000"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 This tool enables editing FCS markers or channels.
61
62 -----
63
64 **Input files**
65
66 This tool requires FCS files as input.
67
68 **Column names**
69
70 Please indicate the names of the markers / channels to edit (comma-separated list).
71
72 .. class:: infomark
73
74 Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
75
76 - Get list of markers and channels in FCS files.
77
78 **Column names**
79
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.
81
82 **Output file**
83
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.
85
86 -----
87
88 **Examples**
89
90 **Input file**::
91
92 Marker1 Marker2 Marker3 Marker4 Marker5
93 4 45 123 1956 62534
94 3 65 104 1254 36576
95 7 26 767 4124 42235
96 4 56 323 7623 74634
97 5 83 532 6256 34763
98 4 15 877 9312 21265
99 ... ... ... ... ...
100
101 *Example 1*
102
103 - Indices: Marker1,Marker3,Marker5
104 - Column names: Marker7,Marker8,Marker9
105
106 *Output1*::
107
108 Marker7 Marker2 Marker8 Marker4 Marker9
109 4 45 123 1956 62534
110 3 65 104 1254 36576
111 7 26 767 4124 42235
112 4 56 323 7623 74634
113 5 83 532 6256 34763
114 4 15 877 9312 21265
115 ... ... ... ... ...
116
117 ]]>
118 </help>
119 </tool>