annotate obistat.xml @ 3:723a93febe89 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"

<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="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>
            <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>
            <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>