Mercurial > repos > immport-devteam > txt_diagnosis

comparison txtDiagnosis.xml @ 1:b94872d65050 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
author azomics
date Thu, 16 Jul 2020 07:35:26 -0400
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0:e1f0194cf8fc 1:b94872d65050
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>