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comparison corr.xml @ 0:62448f26c3fa draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:25:59 -0400
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1 <tool id="csvtk_correlation" name="csvtk-correlation" version="@VERSION@+@GALAXY_VERSION@">
2 <description> calculate pearson correlation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_cmd" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 ###################
11 ## Start Command ##
12 ###################
13
14 csvtk corr --num-cpus "\${GALAXY_SLOTS:-1}"
15
16 ## Add additional flags as specified ##
17 #######################################
18 $global_param.illegal_rows
19 $global_param.empty_rows
20 $global_param.header
21 $global_param.lazy_quotes
22
23 ## Set Tabular input/output flag if input is tabular ##
24 #######################################################
25 #if $in_1.is_of_type("tabular"):
26 -t -T
27 #end if
28
29 ## Specify fields ##
30 ####################
31 -f '$in_text'
32
33 ## Set Input ##
34 ###############
35 '$in_1'
36
37 ## other ##
38 ###########
39 $ignore_nan
40 $log_values
41 $passthrough
42
43 ## To output ##
44 ###############
45 &> corr
46
47 ]]></command>
48 <inputs>
49 <expand macro="singular_input" />
50 <param name="in_text" type="text" argument="-f"
51 label="Specify *two* column names"
52 help="Input the exact spelling of the two input column names wanted with a comma (,) separating them. Ex. 'Length,GC Content'">
53 <expand macro="text_sanitizer" />
54 </param>
55 <param name="ignore_nan" type="boolean" checked="false" argument="-i"
56 truevalue="-i"
57 falsevalue=""
58 label="Ignore non-numeric values in columns"
59 help="Needed to be set to yes to avoid returning NaN if there is a non-numeric value"
60 />
61 <param name="log_values" type="boolean" checked="false" argument="-L"
62 truevalue="-L"
63 falsevalue=""
64 label="Log10 transformed Data"
65 help="Calcute correlations on Log10 transformed data"
66 />
67 <param name="passthrough" type="boolean" checked="false" argument="-x"
68 truevalue="-x"
69 falsevalue=""
70 label="passthrough mode (forward input to output)"
71 />
72 <expand macro="global_parameters" />
73 </inputs>
74 <outputs>
75 <data format_source="in_1" name="corr" from_work_dir="corr" label="${in_1.name} correlation of ${in_text}" />
76 </outputs>
77 <tests>
78 <test>
79 <param name="in_1" value="XY_converted.csv" />
80 <param name="in_text" value="X,Y" />
81 <output name="corr" value="corr_1.csv" />
82 </test>
83 <test>
84 <param name="in_1" value="XY_converted.tsv" />
85 <param name="in_text" value="X,Y" />
86 <param name="ignore_nan" value="true" />
87 <param name="log_values" value="true" />
88 <param name="passthrough" value="true" />
89 <output name="corr" value="corr_2.tsv" />
90 </test>
91 </tests>
92 <help><![CDATA[
93
94 Csvtk - Correlation Help
95 ------------------------
96
97 Info
98 ####
99
100 Csvtk Correlation calculates the pearson correlation between two columns specified by the column header
101
102 .. class:: warningmark
103
104 Single quotes are not allowed in text inputs!
105
106 @HELP_INPUT_DATA@
107
108
109 Usage
110 #####
111
112 To run csvtk-correlation, all you need is a valid (as defined above) CSV or TSV file with two numeric columns that you want to
113 find the pearson correlation between. If the input data is Log10 transformed, remember to set the "Log10 transformed Data"
114 slider to "Yes"
115
116 Output will be a singular line with the input column names, and the pearson correlation (integer between -1 to 1).
117
118
119 **Example Correlation Input**
120
121 Input table:
122
123 +-------+--------+
124 | Group | Length |
125 +=======+========+
126 | 1 | 1500 |
127 +-------+--------+
128 | 2 | 1000 |
129 +-------+--------+
130 | 1 | 1500 |
131 +-------+--------+
132 | 3 | 2000 |
133 +-------+--------+
134
135 Our input for this would require us to specify our column input (-f) as "Group,Length" to allow the program to run
136
137 Our output would then look as such:
138
139 +-------+--------+--------+
140 | Group | Length | 0.9999 |
141 +-------+--------+--------+
142
143 --------
144
145
146 @HELP_COLUMNS@
147
148
149 @HELP_END_STATEMENT@
150
151
152 ]]></help>
153 <expand macro="citations" />
154 </tool>