Mercurial > repos > iuc > obi_stat
comparison obistat.xml @ 4:5f4544915893 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
| author | iuc |
|---|---|
| date | Wed, 20 Mar 2024 13:16:41 +0000 |
| parents | 723a93febe89 |
| children |
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| 3:723a93febe89 | 4:5f4544915893 |
|---|---|
| 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 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="bio_tools"/> | |
| 6 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
| 8 <command><![CDATA[ | 9 <command><![CDATA[ |
| 9 @GUNZIP_INPUT@ | 10 @GUNZIP_INPUT@ |
| 10 | 11 |
| 38 #end if | 39 #end if |
| 39 @INPUT_FORMAT@ | 40 @INPUT_FORMAT@ |
| 40 input > '$output' | 41 input > '$output' |
| 41 ]]></command> | 42 ]]></command> |
| 42 <inputs> | 43 <inputs> |
| 43 <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"/> |
| 44 <repeat name="catattributes" title="Category attribute" min="0"> | 45 <repeat name="catattributes" title="Category attribute" min="0"> |
| 45 <conditional name="options_attributespe"> | 46 <conditional name="options_attributespe"> |
| 46 <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?"> |
| 47 <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> |
| 48 <option value="python">by a python expression</option> | 49 <option value="python">by a python expression</option> |
| 49 </param> | 50 </param> |
| 50 <when value="python"> | 51 <when value="python"> |
| 51 <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."> |
| 52 <expand macro="sanitizer"/> | 53 <expand macro="sanitizer"/> |
| 53 </param> | 54 </param> |
| 54 </when> | 55 </when> |
| 55 <when value="key"> | 56 <when value="key"> |
| 56 <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"> |
| 57 <expand macro="attributes"/> | 58 <expand macro="attributes"/> |
| 58 </param> | 59 </param> |
| 59 </when> | 60 </when> |
| 60 </conditional> | 61 </conditional> |
| 61 </repeat> | 62 </repeat> |
| 62 <conditional name="options_attribute"> | 63 <conditional name="options_attribute"> |
| 63 <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"> |
| 64 <option value="None" selected="true">no</option> | 65 <option value="None" selected="true">no</option> |
| 65 <option value="yes">yes</option> | 66 <option value="yes">yes</option> |
| 66 </param> | 67 </param> |
| 67 <when value="yes"> | 68 <when value="yes"> |
| 68 <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"> |
| 69 <option value="min" selected="true">min</option> | 70 <option value="min" selected="true">min</option> |
| 70 <option value="max">max</option> | 71 <option value="max">max</option> |
| 71 <option value="mean">mean</option> | 72 <option value="mean">mean</option> |
| 72 <option value="variance">variance</option> | 73 <option value="variance">variance</option> |
| 73 <option value="std">standard deviation</option> | 74 <option value="std">standard deviation</option> |
| 74 </param> | 75 </param> |
| 75 <param name="options_uniq_selector" type="select" label="Attribute to merge" > | 76 <param name="options_uniq_selector" type="select" label="Attribute to merge"> |
| 76 <expand macro="attributes"/> | 77 <expand macro="attributes"/> |
| 77 </param> | 78 </param> |
| 78 </when> | 79 </when> |
| 79 <when value="None"></when> | 80 <when value="None"></when> |
| 80 </conditional> | 81 </conditional> |
| 82 </inputs> | 83 </inputs> |
| 83 <outputs> | 84 <outputs> |
| 84 <data format="txt" name="output"/> | 85 <data format="txt" name="output"/> |
| 85 </outputs> | 86 </outputs> |
| 86 <tests> | 87 <tests> |
| 87 <test> | 88 <test expect_num_outputs="1"> |
| 88 <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> | 89 <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> |
| 89 <conditional name="catattributes_0|options_attributespe"> | 90 <conditional name="catattributes_0|options_attributespe"> |
| 90 <param name="options_attributespe_selector" value="key"/> | 91 <param name="options_attributespe_selector" value="key"/> |
| 91 <param name="options_catattribute_selector" value="count" /> | 92 <param name="options_catattribute_selector" value="count" /> |
| 92 </conditional> | 93 </conditional> |
| 99 <param name="options_attribute_selector" value="min" /> | 100 <param name="options_attribute_selector" value="min" /> |
| 100 <param name="options_uniq_selector" value="seq_length" /> | 101 <param name="options_uniq_selector" value="seq_length" /> |
| 101 </conditional> | 102 </conditional> |
| 102 <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> | 103 <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> |
| 103 </test> | 104 </test> |
| 104 <test> | 105 <test expect_num_outputs="1"> |
| 105 <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> | 106 <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> |
| 106 <conditional name="catattributes_0|options_attributespe"> | 107 <conditional name="catattributes_0|options_attributespe"> |
| 107 <param name="options_attributespe_selector" value="key"/> | 108 <param name="options_attributespe_selector" value="key"/> |
| 108 <param name="options_catattribute_selector" value="count" /> | 109 <param name="options_catattribute_selector" value="count" /> |
| 109 </conditional> | 110 </conditional> |