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comparison obistat.xml @ 3:723a93febe89 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:37:00 +0000
parents 65bb66b261e3
children 5f4544915893
comparison
equal deleted inserted replaced
2:39320fee9d70 3:723a93febe89
1 <tool id="obi_stat" name="obistat" version="@TOOL_VERSION@"> 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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 8 <command><![CDATA[
9 <command> 9 @GUNZIP_INPUT@
10
11 <![CDATA[
12 10
13 obistat 11 obistat
12 --without-progress-bar
14 #for $attribute in $catattributes 13 #for $attribute in $catattributes
15 #if str( $attribute.options_attributespe.options_attributespe_selector) == "key" 14 #if str( $attribute.options_attributespe.options_attributespe_selector) == "key"
16 -c '$attribute.options_attributespe.options_catattribute_selector' 15 -c '$attribute.options_attributespe.options_catattribute_selector'
17 #end if 16 #end if
18 #if str( $attribute.options_attributespe.options_attributespe_selector) == "python" 17 #if str( $attribute.options_attributespe.options_attributespe_selector) == "python"
35 #end if 34 #end if
36 #if str( $options_attribute.options_attribute_selector) == "std" 35 #if str( $options_attribute.options_attribute_selector) == "std"
37 -s '$options_attribute.options_uniq_selector' 36 -s '$options_attribute.options_uniq_selector'
38 #end if 37 #end if
39 #end if 38 #end if
40 39 @INPUT_FORMAT@
41 '$input' > '$output' 40 input > '$output'
42 41 ]]></command>
43 ]]>
44
45
46 </command>
47
48 <inputs> 42 <inputs>
49 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" /> 43 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
50
51 <repeat name="catattributes" title="Category attribute" min="0"> 44 <repeat name="catattributes" title="Category attribute" min="0">
52 <conditional name="options_attributespe"> 45 <conditional name="options_attributespe">
53 <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" > 46 <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> 47 <option value="key" selected="true">simply by a key of an attribute</option>
55 <option value="python">by a python expression</option> 48 <option value="python">by a python expression</option>
64 <expand macro="attributes"/> 57 <expand macro="attributes"/>
65 </param> 58 </param>
66 </when> 59 </when>
67 </conditional> 60 </conditional>
68 </repeat> 61 </repeat>
69
70 <conditional name="options_attribute"> 62 <conditional name="options_attribute">
71 <param name="options_attributebe_selector" type="select" label="Use a specific option" > 63 <param name="options_attributebe_selector" type="select" label="Use a specific option" >
72 <option value="None" selected="true">no</option> 64 <option value="None" selected="true">no</option>
73 <option value="yes">yes</option> 65 <option value="yes">yes</option>
74 </param> 66 </param>
84 <expand macro="attributes"/> 76 <expand macro="attributes"/>
85 </param> 77 </param>
86 </when> 78 </when>
87 <when value="None"></when> 79 <when value="None"></when>
88 </conditional> 80 </conditional>
81 <expand macro="input_format_options_macro"/>
89 </inputs> 82 </inputs>
90 <outputs> 83 <outputs>
91 <data format="txt" name="output" label="output.txt with ${tool.name} on ${on_string}" /> 84 <data format="txt" name="output"/>
92 </outputs> 85 </outputs>
93 <tests> 86 <tests>
94 <test> 87 <test>
95 <param name="input" value="output_obiannotate.fasta" /> 88 <param name="input" value="output_obiannotate.fasta" ftype="fasta"/>
89 <conditional name="catattributes_0|options_attributespe">
90 <param name="options_attributespe_selector" value="key"/>
91 <param name="options_catattribute_selector" value="count" />
92 </conditional>
93 <conditional name="catattributes_1|options_attributespe">
94 <param name="options_attributespe_selector" value="key"/>
95 <param name="options_catattribute_selector" value="merged" />
96 </conditional>
97 <conditional name="options_attribute">
98 <param name="options_attributebe_selector" value="yes"/>
99 <param name="options_attribute_selector" value="min" />
100 <param name="options_uniq_selector" value="seq_length" />
101 </conditional>
102 <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/>
103 </test>
104 <test>
105 <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" />
96 <conditional name="catattributes_0|options_attributespe"> 106 <conditional name="catattributes_0|options_attributespe">
97 <param name="options_attributespe_selector" value="key"/> 107 <param name="options_attributespe_selector" value="key"/>
98 <param name="options_catattribute_selector" value="count" /> 108 <param name="options_catattribute_selector" value="count" />
99 </conditional> 109 </conditional>
100 <conditional name="catattributes_1|options_attributespe"> 110 <conditional name="catattributes_1|options_attributespe">