annotate obistat.xml @ 0:ee9cd37c2f3d draft

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