Mercurial > repos > iuc > obi_stat
comparison obistat.xml @ 3:723a93febe89 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author | iuc |
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date | Mon, 10 May 2021 19:37:00 +0000 |
parents | 65bb66b261e3 |
children | 5f4544915893 |
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2:39320fee9d70 | 3:723a93febe89 |
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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"> |