annotate gblocks.xml @ 0:daf61c79c8b4 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33

<tool id="gblocks" name="Gblocks" version="0.91b">
    <description>Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis</description>
    <requirements>
        <requirement type="package" version="0.91b">gblocks</requirement>
    </requirements>
    <command><![CDATA[
ln -s '$inputFile' input.pir && Gblocks
input.pir
-t=$t
#if $advanced.a == '-a'
    #if str($advanced.b1)
        -b1=$advanced.b1
    #end if
    #if str($advanced.b2)
        -b2=$advanced.b2
    #end if
    -b3=$advanced.b3
    -b4=$advanced.b4
    -b5=$advanced.b5
    -b6=$advanced.b6
    -b0=$advanced.b0
#end if
#set $output_opt = ''
#if $outputs
    #set $outputs_arr = str($outputs).split(',')
    #for $o in $outputs_arr
        #set $output_opt += $o + '=y '
    #end for
#else
    #set $outputs_arr = []
#end if
#if $output_opt
    #set $output_opt = $output_opt[:-1]
#end if
$output_opt
> '$outputFile'
    ]]></command>
    <inputs>
        <param name="inputFile" type="data" format="fasta,pir" label="Multiple Sequence Alignment" help="Multiple Sequence Alignment in Fasta format." />
        <param argument="-t" type="select" label="Type Of Sequence">
            <option value="p" selected="true">Protein</option>
            <option value="d">DNA</option>
            <option value="c">Codons</option>
        </param>
        <conditional name="advanced">
            <param name="a" type="select" label="Specify Advanced Parameters">
                <option value="-a">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <when value="" />
            <when value="-a">
                <param argument="-b1" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a conserved position" help="Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences" />
                <param argument="-b2" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a flank position" help="Any integer equal or bigger than minimum number of sequences for a conserved position" />
                <param argument="-b3" type="integer" value="8" label="Maximum number of contiguous nonconserved positions" />
                <param argument="-b4" type="integer" value="10" min="2" label="Minimum length of a block" />
                <param argument="-b5" type="select" label="Allowed gap positions">
                    <option value="n" selected="true">None</option>
                    <option value="h">With Half</option>
                    <option value="a">All</option>
                </param>
                <param argument="-b6" type="select" label="Use similarity matrices">
                    <option value="y" selected="true">Yes</option>
                    <option value="n">No</option>
                </param>
                <param argument="-b0" type="integer" value="10" min="2" label="Minimum length of an intial block" />
            </when>
        </conditional> 
        <param name="outputs" type="select" multiple="true" optional="true" display="checkboxes" label="Output formats">
            <option value="-s" selected="true">Selected blocks</option>
            <option value="-p" selected="true">Results and parameters File</option>
            <option value="-n">Nonconserved blocks</option>
            <option value="-u">Ungapped alignment</option>
            <option value="-k">Mask file with the selected blocks</option>
            <option value="-d">Postscript file with the selected blocks</option>
        </param>
    </inputs>
    <outputs>
        <data name="outputFile" format="txt" label="${tool.name} on ${on_string}" />
        <data name="Results_and_parameters_file" format="html" from_work_dir="input.pir-gb.htm" label="${tool.name} Results and parameters on ${on_string}" >
            <filter>outputs and '-p' in outputs</filter>
        </data>
        <data name="Selected_blocks" format="txt" from_work_dir="input.pir-gb" label="${tool.name} Selected blocks on ${on_string}" >
            <filter>outputs and '-s' in outputs</filter>
        </data>
        <data name="Nonconserved_blocks" format="txt" from_work_dir="input.pir-gbComp" label="${tool.name} Nonconserved blocks on ${on_string}" >
            <filter>outputs and '-n' in outputs</filter>
        </data>
        <data name="Ungapped_alignment" format="txt" from_work_dir="input.pir--" label="${tool.name} Ungapped alignment on ${on_string}" >
            <filter>outputs and '-u' in outputs</filter>
        </data>
        <data name="Masked_file_with_the_selected_blocks" format="txt" from_work_dir="input.pir-gbMask" label="${tool.name} Masked file with the selected blocks on ${on_string}" >
            <filter>outputs and '-k' in outputs</filter>
        </data>
        <data name="Postscript_file_with_the_selected_blocks" format="eps" from_work_dir="input.pir-gbPS" label="${tool.name} Postscript on ${on_string}" >
            <filter>outputs and '-d' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" ftype="fasta" value="nad3.fasta" />
            <param name="-t" value="p" />
            <param name="outputs" value="-s,-p" />
            <output name="outputFile" file="Gblocks_on_data_95.txt" />
            <output name="Results_and_parameters_file" file="Gblocks_Results_And_Parameters_on_data_95_html.html" />
            <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
        </test>
        <test>
            <param name="inputFile" ftype="fasta" value="nad3.fasta" />
            <param name="-t" value="p" />
            <param name="outputs" value="-s" />
            <output name="outputFile" file="Gblocks_on_data_95.txt" />
            <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
        </test>
    </tests>
    <help><![CDATA[
Simple wrapper for `Gblocks`_. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

.. _Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
    ]]></help>
    <citations>
        <citation type="doi">10.1093/oxfordjournals.molbev.a026334</citation>
    </citations>
</tool>