Mercurial > repos > immport-devteam > check_fcs_headers

comparison getFCSheaders.xml @ 1:a5609a84ed16 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit e5be067c50262354a028bd03b77beb8369fb6fb1"
author azomics
date Thu, 23 Jul 2020 08:14:29 -0400
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0:d3957a51cc51 1:a5609a84ed16
1 <tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0">
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="warning" description="Not all files are valid FCS files, see output for details." />
8 </stdio>
9 <command><![CDATA[
10 Rscript '$__tool_directory__/getFCSheader.R' '${output_file}'
11 #for $f in $input
12 '${f}' '${f.name}'
13 #end for
14 ]]>
15 </command>
16 <inputs>
17 <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
18 </inputs>
19 <outputs>
20 <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="input">
25 <collection type="list">
26 <element name="input1.fcs" value="input1.fcs"/>
27 <element name="input2.fcs" value="input2.fcs"/>
28 <element name="input3.fcs" value="input3.fcs"/>
29 </collection>
30 </param>
31 <output name="output_file" file="output.tabular" lines_diff="8"/>
32 </test>
33 </tests>
34 <help><![CDATA[
35 This tool returns a table of the headers of a set of FCS files.
36
37 -----
38
39 **Input files**
40
41 This tool requires collections of FCS files as input.
42
43 **Output file**
44
45 The output file is a table listing the markers and channels for each file.
46
47 -----
48
49 **Example**
50
51 *File1*::
52
53 Marker1 Marker2 Marker3
54 34 45 12
55 33 65 10
56
57 *File2*::
58
59 Marker4 Marker5 Marker3
60 19 62 98
61 12 36 58
62
63 *Output*::
64
65 Filename Index 1 2 3
66 File1 channels Channel1 Channel2 Channel3
67 File2 channels Channel4 Channel5 Channel3
68 File1 markers Marker1 Marker2 Marker3
69 File2 markers Marker4 Marker5 Marker3
70 ]]>
71 </help>
72 </tool>