Mercurial > repos > immport-devteam > txt_diagnosis
comparison txtDiagnosis.xml @ 1:b94872d65050 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
author | azomics |
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date | Thu, 16 Jul 2020 07:35:26 -0400 |
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0:e1f0194cf8fc | 1:b94872d65050 |
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1 <tool id="txt_diagnosis" name="Check data" version="1.1+galaxy0" profile="18.01"> | |
2 <description> in txt-converted FCS files</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.17.1">pandas</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" /> | |
8 </stdio> | |
9 <command><![CDATA[ | |
10 python '$__tool_directory__/txtdiagnosis.py' -i '${input}' -o '${output}' -n '${input.name}' | |
11 ]]> | |
12 </command> | |
13 <inputs> | |
14 <param format="flowtext" name="input" type="data" label="Text file to check"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="txt" name="output" label="Report on ${input.name}"/> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <param name="input" value="input_error.txt"/> | |
22 <output name="output" file="output_error.txt"> | |
23 <assert_contents> | |
24 <has_text_matching expression="WARNING: line 6 in .* contains non-numeric results"/> | |
25 </assert_contents> | |
26 </output> | |
27 </test> | |
28 <test> | |
29 <param name="input" value="input_noerror.txt"/> | |
30 <output name="output" file="output_noerror.txt"> | |
31 <assert_contents> | |
32 <has_text text="No errors in the file."/> | |
33 </assert_contents> | |
34 </output> | |
35 </test> | |
36 </tests> | |
37 <help><![CDATA[ | |
38 This tool looks for potential errors in txt-converted FCS files. | |
39 ----- | |
40 **Input** | |
41 This diagnosis tools reads in text files, and checks that the data is all numeric. | |
42 **Output** | |
43 The output is a report with the errors and corresponding line numbers. | |
44 ----- | |
45 **Example** | |
46 *Input*:: | |
47 Marker1 Marker2 Marker3 | |
48 34 45 12 | |
49 NaN 65 10 | |
50 34 45 12 | |
51 33 NaN 10 | |
52 34 45 12 | |
53 33 65 10 | |
54 34 45 12 | |
55 33 65 NaN | |
56 34 45 12 | |
57 33 65 10 | |
58 *Output*:: | |
59 WARNING: line 2 in example_file.txt contains non-numeric results | |
60 WARNING: line 4 in example_file.txt contains non-numeric results | |
61 WARNING: line 8 in example_file.txt contains non-numeric results | |
62 ]]> | |
63 </help> | |
64 </tool> |