Mercurial > repos > azomics > metacyto_checkpanel

comparison metacyto_checkpanel.xml @ 0:67d79ba0f7aa draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
author azomics
date Tue, 27 Jul 2021 21:47:56 +0000
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1 <tool id="metacyto_checkpanel" name="Check markers in analysis panels" version="1.0+galaxy0" profile="18.01">
2 <description>for MetaCyto</description>
3 <requirements>
4 <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:9" />
8 <exit_code range="10" level="fatal" description="The input file cannot be used. Please check input format." />
9 <exit_code range="11:" />
10 </stdio>
11 <command><![CDATA[
12 Rscript --slave --vanilla '$__tool_directory__/metacyto_checkpanel.R' '${input_file}' '${output_file}';
13 #if $graph=="TRUE"
14 mv panel_summary.pdf '${pdf_out}'
15 #end if
16 ]]>
17 </command>
18 <inputs>
19 <param format="metacyto_summary.txt" name="input_file" type="data" label="MetaCyto preprocessing summary"/>
20 <param name="graph" type="boolean" label="Output visual summary?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
21 </inputs>
22 <outputs>
23 <data format="tabular" name="output_file" label="Panel Summary of ${input_file.name}"/>
24 <data format="pdf" name="pdf_out" label="Visual Panel Summary of ${input_file.name}">
25 <filter>(graph)</filter>
26 </data>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input_file" value="mc_preprocesss_summary.metacyto_summary.txt"/>
31 <param name="graph" value="True"/>
32 <output name="output_file" ftype="tabular">
33 <assert_contents>
34 <has_n_columns n="3" />
35 <has_text text="CD95" />
36 <has_n_lines n="14" />
37 </assert_contents>
38 </output>
39 <output name="pdf_out" ftype="pdf">
40 <assert_contents>
41 <has_size value="4569" delta="500" />
42 </assert_contents>
43 </output>
44 </test>
45 </tests>
46 <help><![CDATA[
47 Metacyto Check Markers in analysis panels
48 -----------------------------------------
49
50 This tool uses MetaCyto's panel summary function to compare marker names between groups of FCS files.
51
52 **Input**
53 This tool requires the MetaCyto pre-processing Summary as input.
54
55 **Output**
56 This tool generates a table and an optional visual representation in PDF of how markers are distributed in the FCS file sets.
57
58
59 **Example**
60
61 *Input* - Summary Table::
62
63 study_id antibodies filenames
64 group1 Marker1|Marker2|Marker3|... file1.fcs
65 group2 Marker1|Marker2|Marker3|... file2.fcs
66 ... ... ...
67
68 *Output* - Panel Summary::
69
70 Markers group1 group2 ...
71 Marker1 1 1 ...
72 Marker2 1 1 ...
73 Marker3 0 1 ...
74 ... ... ... ...
75
76 *Graphical output*
77
78 .. image:: ./images/checkpanel.png
79 ]]>
80 </help>
81 </tool>