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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33
author | earlhaminst |
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date | Thu, 12 Apr 2018 06:59:23 -0400 |
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<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>