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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:27:29 -0400
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38e2b656eb28 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 <tool id="lucy" name="LUCY trimmer" version='1.0.1' description="Less Useful Chunks Yank">
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2 <command interpreter='perl'>psub -l galaxy_normal.c --fasta $fasta_infile --cat $fasta_outfile --cat $qual_outfile
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3 lucy -quiet -xtra 8
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4 -error $max_avg_error $max_error_at_ends
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5 -bracket $bracket_window_size $bracket_max_avg_error
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6 #if $vector.vector_select == '1':
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7 -vector $vector.vector_fasta_infile $vector.splice_fasta_infile
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8 #end if
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9 -output $fasta_outfile $qual_outfile
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10 $fasta_infile $qual_infile
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11 </command>
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12
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13 <inputs>
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14 <param name="fasta_infile" type="data" format="fasta" label="Read sequences (Fasta)"/>
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15 <param name="qual_infile" type="data" format="qual454" label="Qual scores input file (qual454)"/>
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16 <param name="max_avg_error" type="text" value='.007' label="max average error"/>
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17 <param name="max_error_at_ends" type="text" value='.007' label="max error at ends"/>
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18 <param name="bracket_window_size" type="integer" value='20' label="bracket window size"/>
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19 <param name="bracket_max_avg_error" type="text" value='.007' label="bracket max average error"/>
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20
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21 <conditional name='vector'>
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22 <param name="vector_select" type="select" label="Do you have vector sequence files?" >
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23 <option value="0">no, just trim by quality alone</option>
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24 <option value="1">yes</option>
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25 </param>
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26 <when value='1'>
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27 <param name="vector_fasta_infile" type="data" format="fasta" label="Complete cloning vector sequence (Fasta)"/>
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28 <param name="splice_fasta_infile" type="data" format="fasta" label="Subsequence before and after each insert site (Fasta)"/>
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29 </when>
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30 <when value='0'>
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31 </when>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <data name="fasta_outfile" format="fasta"/>
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36 <data name="qual_outfile" format="qual454"/>
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37 </outputs>
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38 <help>
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39 Less Useful Chunks Yank (lucy) is a utility that prepares raw DNA sequence fragments for sequence assembly.
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40 It performs quality end-trimming and optionally removal of primer/vector sequences or filtering contamination.
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41
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42 ---
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43
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44 Each sequence in the output sequence file begins with a header that includes its name, three pass along
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45 clone length values to the fragment assembly program, and a left and right marker denoting the begin and
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46 end of the good quality, vector free region. The following is an example of lucy output::
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47
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48 &gt;GCCAA03TF 1500 3000 2000 43 490
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49 AGCCAAGTTTGCAGCCCTGCAGGTCGACTCTAGAGGATCCCCAGGATGATCAGCCACATT
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50 GGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGG
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51 GCGAAAGCCTGACGCAGCCATGCCGCGTGAATGATGAAGGTCTTAGGATTGTAAAATTCT
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52 TTCACCGGGGACGATAATGACGGTACCCGGAGAAGAAGCCCCGGCTAACTTCGTGCCAGC
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53 ...
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54
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55 ---
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56
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57 **Manual**
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58
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59 http://galaxy.jgi-psf.org/static/manuals/lucy.pdf
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60
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61 </help>
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62 </tool>