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comparison obistat.xml @ 0:ee9cd37c2f3d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:38:35 -0400
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children 65bb66b261e3
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-1:000000000000 0:ee9cd37c2f3d
1 <tool id="obi_stat" name="obistat" version="@WRAPPER_VERSION@">
2 <description>computes basic statistics for attribute values</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8
9 <command>
10
11 <![CDATA[
12
13 obistat
14 #for $attribute in $catattributes
15 #if str( $attribute.options_attributespe.options_attributespe_selector) == "key"
16 -c '$attribute.options_attributespe.options_catattribute_selector'
17 #end if
18 #if str( $attribute.options_attributespe.options_attributespe_selector) == "python"
19 -c '${attribute.options_attributespe.attribute}'
20 #end if
21 #end for
22
23 #if str( $options_attribute.options_attributebe_selector) == "yes"
24 #if str( $options_attribute.options_attribute_selector) == "min"
25 -m '$options_attribute.options_uniq_selector'
26 #end if
27 #if str( $options_attribute.options_attribute_selector) == "max"
28 -M '$options_attribute.options_uniq_selector'
29 #end if
30 #if str( $options_attribute.options_attribute_selector) == "mean"
31 -a '$options_attribute.options_uniq_selector'
32 #end if
33 #if str( $options_attribute.options_attribute_selector) == "variance"
34 -v '$options_attribute.options_uniq_selector'
35 #end if
36 #if str( $options_attribute.options_attribute_selector) == "std"
37 -s '$options_attribute.options_uniq_selector'
38 #end if
39 #end if
40
41 '$input' > '$output'
42
43 ]]>
44
45
46 </command>
47
48 <inputs>
49 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" />
50
51 <repeat name="catattributes" title="Category attribute" min="0">
52 <conditional name="options_attributespe">
53 <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" >
54 <option value="key" selected="true">simply by a key of an attribute</option>
55 <option value="python">by a python expression</option>
56 </param>
57 <when value="python">
58 <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive." >
59 <expand macro="sanitizer"/>
60 </param>
61 </when>
62 <when value="key">
63 <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records" >
64 <expand macro="attributes"/>
65 </param>
66 </when>
67 </conditional>
68 </repeat>
69
70 <conditional name="options_attribute">
71 <param name="options_attributebe_selector" type="select" label="Use a specific option" >
72 <option value="None" selected="true">no</option>
73 <option value="yes">yes</option>
74 </param>
75 <when value="yes">
76 <param name="options_attribute_selector" type="select" label="Select your specific option" >
77 <option value="min" selected="true">min</option>
78 <option value="max">max</option>
79 <option value="mean">mean</option>
80 <option value="variance">variance</option>
81 <option value="std">standard deviation</option>
82 </param>
83 <param name="options_uniq_selector" type="select" label="Attribute to merge" >
84 <expand macro="attributes"/>
85 </param>
86 </when>
87 <when value="None"></when>
88 </conditional>
89 </inputs>
90 <outputs>
91 <data format="txt" name="output" label="output.txt with ${tool.name} on ${on_string}" />
92 </outputs>
93 <tests>
94 <test>
95 <param name="input" value="output_obiannotate.fasta" />
96 <conditional name="catattributes_0|options_attributespe">
97 <param name="options_attributespe_selector" value="key"/>
98 <param name="options_catattribute_selector" value="count" />
99 </conditional>
100 <conditional name="catattributes_1|options_attributespe">
101 <param name="options_attributespe_selector" value="key"/>
102 <param name="options_catattribute_selector" value="merged" />
103 </conditional>
104 <conditional name="options_attribute">
105 <param name="options_attributebe_selector" value="yes"/>
106 <param name="options_attribute_selector" value="min" />
107 <param name="options_uniq_selector" value="seq_length" />
108 </conditional>
109
110 <output name="output" file="output_obistat.txt" ftype="txt"/>
111 </test>
112 </tests>
113 <help><![CDATA[
114
115 .. class:: infomark
116
117 **What it does**
118
119 stats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like:
120
121 \* minimum value (-m option)
122
123 \* maximum value (-M option)
124
125 \* mean value (-a option)
126
127 \* variance (-v option)
128
129 \* standard deviation (-s option)
130
131 The result is a contingency table with the different categories in rows, and the computed statistics in columns.
132
133 @OBITOOLS_LINK@
134
135 ]]>
136 </help>
137 <expand macro="citation" />
138 </tool>