Mercurial > repos > earlhaminst > gblocks
diff gblocks.xml @ 0:daf61c79c8b4 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33
| author | earlhaminst |
|---|---|
| date | Thu, 12 Apr 2018 06:59:23 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gblocks.xml Thu Apr 12 06:59:23 2018 -0400 @@ -0,0 +1,123 @@ +<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>