Mercurial > repos > eremeeva > sibelia
diff tools/sibelia/init_sibelia.xml @ 5:7b5e87542bd8 draft default tip
Coming to conclusion. Testing.
author | eremeevaaa94@mail.ru |
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date | Sun, 13 Apr 2014 07:02:26 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/sibelia/init_sibelia.xml Sun Apr 13 07:02:26 2014 -0700 @@ -0,0 +1,58 @@ +<tool id="Sibelia" name="sibelia"> + <command interpreter="python"> + #if $p_s.p_s_select == "-s" #Sibelia_wrapper.py -s $p_s.simplification $ram -m $b_size $single_ou $postprocess -i $iter $fasta + #else #Sibelia_wrapper.py -k $p_s.cpfile $ram -m $b_size $single_ou $postprocess -i $iter $fasta + #end if# + </command> + <inputs> + <conditional name="p_s"> + <param name="p_s_select" type="select" label="Parameters set"> + <option value="-s">Select parameters set</option> + <option value="-k">Custom parameteres set</option> + </param> + <when value="-k"> + <param name="cpfile" size="50" type="text" label="File of custom parameters set" /> + </when> + <when value="-s"> + <param name="simplification" type="select" label="Simplification"> + <option value="loose">Loose</option> + <option value="fine">Fine</option> + </param> + </when> + </conditional> + <param name="ram" type="boolean" truevalue="-r" falsevalue="" label="Store temporary files in RAM?" /> + <param name="single_ou" type="boolean" truevalue="-a" falsevalue="" label="Find blocks that occur exactly once in each input sequence" /> + <param name="postprocess" type="boolean" truevalue="--nopostprocess" falsevalue="" label="Turn off postprocessing?" /> + <param name="iter" type="integer" value="4" label="Number of iterations" /> + <param name="b_size" type="integer" value="2000" label="Minimum block size" /> + <param name="fasta" size="50" type="text" label="Path to input fasta file" /> + </inputs> + <outputs> + <data format="txt" name="outperm" label="Genomes permutations" from_work_dir="genomes_permutations.txt" /> + <data format="txt" name="outblc" label="Blocks coords" from_work_dir="blocks_coords.txt" /> + <data format="txt" name="outcov" label="Coverage report" from_work_dir="coverage_report.txt" /> + <data format="html" name="outbld" label="Blocks diagram" from_work_dir="d3_blocks_diagram.html" /> + </outputs> + <!-- <tests> + <test> + <param name="p_s_select" value="-s" /> + <param name="simplification" value="loose" /> + <param name="ram" value="0" /> + <param name="single_ou" value="0" /> + <param name="postprocess" value="0" /> + <param name="fasta" value="Helicobacter_pylori.fasta" /> + </test> + <test> + <param name="p_s_select" value="-k" /> + <param name="cpfile" value="CPFile.txt" /> + <param name="ram" value="0" /> + <param name="single_ou" value="0" /> + <param name="postprocess" value="0" /> + <param name="fasta" value="Helicobacter_pylori.fasta" /> + </test> + </tests> --> + <help> + .. class:: infomark + Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks. + </help> +</tool> \ No newline at end of file