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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author | iuc |
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date | Wed, 20 Mar 2024 13:16:41 +0000 |
parents | 723a93febe89 |
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<tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>computes basic statistics for attribute values</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @GUNZIP_INPUT@ obistat --without-progress-bar #for $attribute in $catattributes #if str( $attribute.options_attributespe.options_attributespe_selector) == "key" -c '$attribute.options_attributespe.options_catattribute_selector' #end if #if str( $attribute.options_attributespe.options_attributespe_selector) == "python" -c '${attribute.options_attributespe.attribute}' #end if #end for #if str( $options_attribute.options_attributebe_selector) == "yes" #if str( $options_attribute.options_attribute_selector) == "min" -m '$options_attribute.options_uniq_selector' #end if #if str( $options_attribute.options_attribute_selector) == "max" -M '$options_attribute.options_uniq_selector' #end if #if str( $options_attribute.options_attribute_selector) == "mean" -a '$options_attribute.options_uniq_selector' #end if #if str( $options_attribute.options_attribute_selector) == "variance" -v '$options_attribute.options_uniq_selector' #end if #if str( $options_attribute.options_attribute_selector) == "std" -s '$options_attribute.options_uniq_selector' #end if #end if @INPUT_FORMAT@ input > '$output' ]]></command> <inputs> <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/> <repeat name="catattributes" title="Category attribute" min="0"> <conditional name="options_attributespe"> <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?"> <option value="key" selected="true">simply by a key of an attribute</option> <option value="python">by a python expression</option> </param> <when value="python"> <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."> <expand macro="sanitizer"/> </param> </when> <when value="key"> <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records"> <expand macro="attributes"/> </param> </when> </conditional> </repeat> <conditional name="options_attribute"> <param name="options_attributebe_selector" type="select" label="Use a specific option"> <option value="None" selected="true">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="options_attribute_selector" type="select" label="Select your specific option"> <option value="min" selected="true">min</option> <option value="max">max</option> <option value="mean">mean</option> <option value="variance">variance</option> <option value="std">standard deviation</option> </param> <param name="options_uniq_selector" type="select" label="Attribute to merge"> <expand macro="attributes"/> </param> </when> <when value="None"></when> </conditional> <expand macro="input_format_options_macro"/> </inputs> <outputs> <data format="txt" name="output"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> <conditional name="catattributes_0|options_attributespe"> <param name="options_attributespe_selector" value="key"/> <param name="options_catattribute_selector" value="count" /> </conditional> <conditional name="catattributes_1|options_attributespe"> <param name="options_attributespe_selector" value="key"/> <param name="options_catattribute_selector" value="merged" /> </conditional> <conditional name="options_attribute"> <param name="options_attributebe_selector" value="yes"/> <param name="options_attribute_selector" value="min" /> <param name="options_uniq_selector" value="seq_length" /> </conditional> <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> </test> <test expect_num_outputs="1"> <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> <conditional name="catattributes_0|options_attributespe"> <param name="options_attributespe_selector" value="key"/> <param name="options_catattribute_selector" value="count" /> </conditional> <conditional name="catattributes_1|options_attributespe"> <param name="options_attributespe_selector" value="key"/> <param name="options_catattribute_selector" value="merged" /> </conditional> <conditional name="options_attribute"> <param name="options_attributebe_selector" value="yes"/> <param name="options_attribute_selector" value="min" /> <param name="options_uniq_selector" value="seq_length" /> </conditional> <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** 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: \* minimum value (-m option) \* maximum value (-M option) \* mean value (-a option) \* variance (-v option) \* standard deviation (-s option) The result is a contingency table with the different categories in rows, and the computed statistics in columns. @OBITOOLS_LINK@ ]]> </help> <expand macro="citation" /> </tool>