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comparison obistat.xml @ 5:ce8fe725383f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
author iuc
date Thu, 30 Oct 2025 16:02:31 +0000
parents 05619490a210
children
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equal deleted inserted replaced
4:05619490a210 5:ce8fe725383f
1 <tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>computes basic statistics for attribute values</description> 2 <description>computes basic statistics for attribute values</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @GUNZIP_INPUT@ 10 @GUNZIP_INPUT@
11 11
39 #end if 39 #end if
40 @INPUT_FORMAT@ 40 @INPUT_FORMAT@
41 input > '$output' 41 input > '$output'
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> 44 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
45 <repeat name="catattributes" title="Category attribute" min="0"> 45 <repeat name="catattributes" title="Category attribute" min="0">
46 <conditional name="options_attributespe"> 46 <conditional name="options_attributespe">
47 <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" > 47 <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?">
48 <option value="key" selected="true">simply by a key of an attribute</option> 48 <option value="key" selected="true">simply by a key of an attribute</option>
49 <option value="python">by a python expression</option> 49 <option value="python">by a python expression</option>
50 </param> 50 </param>
51 <when value="python"> 51 <when value="python">
52 <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." > 52 <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.">
53 <expand macro="sanitizer"/> 53 <expand macro="sanitizer"/>
54 </param> 54 </param>
55 </when> 55 </when>
56 <when value="key"> 56 <when value="key">
57 <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records" > 57 <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records">
58 <expand macro="attributes"/> 58 <expand macro="attributes"/>
59 </param> 59 </param>
60 </when> 60 </when>
61 </conditional> 61 </conditional>
62 </repeat> 62 </repeat>
63 <conditional name="options_attribute"> 63 <conditional name="options_attribute">
64 <param name="options_attributebe_selector" type="select" label="Use a specific option" > 64 <param name="options_attributebe_selector" type="select" label="Use a specific option">
65 <option value="None" selected="true">no</option> 65 <option value="None" selected="true">no</option>
66 <option value="yes">yes</option> 66 <option value="yes">yes</option>
67 </param> 67 </param>
68 <when value="yes"> 68 <when value="yes">
69 <param name="options_attribute_selector" type="select" label="Select your specific option" > 69 <param name="options_attribute_selector" type="select" label="Select your specific option">
70 <option value="min" selected="true">min</option> 70 <option value="min" selected="true">min</option>
71 <option value="max">max</option> 71 <option value="max">max</option>
72 <option value="mean">mean</option> 72 <option value="mean">mean</option>
73 <option value="variance">variance</option> 73 <option value="variance">variance</option>
74 <option value="std">standard deviation</option> 74 <option value="std">standard deviation</option>
75 </param> 75 </param>
76 <param name="options_uniq_selector" type="select" label="Attribute to merge" > 76 <param name="options_uniq_selector" type="select" label="Attribute to merge">
77 <expand macro="attributes"/> 77 <expand macro="attributes"/>
78 </param> 78 </param>
79 </when> 79 </when>
80 <when value="None"></when> 80 <when value="None"></when>
81 </conditional> 81 </conditional>
83 </inputs> 83 </inputs>
84 <outputs> 84 <outputs>
85 <data format="txt" name="output"/> 85 <data format="txt" name="output"/>
86 </outputs> 86 </outputs>
87 <tests> 87 <tests>
88 <test> 88 <test expect_num_outputs="1">
89 <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> 89 <param name="input" value="output_obiannotate.fasta" ftype="fasta"/>
90 <conditional name="catattributes_0|options_attributespe"> 90 <conditional name="catattributes_0|options_attributespe">
91 <param name="options_attributespe_selector" value="key"/> 91 <param name="options_attributespe_selector" value="key"/>
92 <param name="options_catattribute_selector" value="count" /> 92 <param name="options_catattribute_selector" value="count" />
93 </conditional> 93 </conditional>
100 <param name="options_attribute_selector" value="min" /> 100 <param name="options_attribute_selector" value="min" />
101 <param name="options_uniq_selector" value="seq_length" /> 101 <param name="options_uniq_selector" value="seq_length" />
102 </conditional> 102 </conditional>
103 <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> 103 <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/>
104 </test> 104 </test>
105 <test> 105 <test expect_num_outputs="1">
106 <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> 106 <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" />
107 <conditional name="catattributes_0|options_attributespe"> 107 <conditional name="catattributes_0|options_attributespe">
108 <param name="options_attributespe_selector" value="key"/> 108 <param name="options_attributespe_selector" value="key"/>
109 <param name="options_catattribute_selector" value="count" /> 109 <param name="options_catattribute_selector" value="count" />
110 </conditional> 110 </conditional>