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annotate velvetg.xml @ 0:c170448acc8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:02:53 -0500
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children c397035f715d
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c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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1 <tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.0">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Velvet sequence assembler for very short reads</description>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <version_command>velvetg 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 <import>macros.xml</import>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 </macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <expand macro="requirements"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <expand macro="stdio"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <command interpreter="python">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 velvetg_wrapper.py
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 '$input.extra_files_path'
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 #if $generate_amos.afg == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 -amos_file $generate_amos.afg
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 #if $unused_reads.generate_unused == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 -unused_reads $unused_reads.generate_unused
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 $read_trkg
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 #if $coverage.cutoff == "auto":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 -cov_cutoff auto
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 #elif $coverage.cutoff == "value":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 -cov_cutoff $coverage.cov_cutoff
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 #if $expected.coverage == "auto":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 -exp_cov auto
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 #elif $expected.coverage == "value":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 -exp_cov $expected.exp_cov
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 #if $contig_lgth.use_contig_lgth == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 -min_contig_lgth $contig_lgth.min_contig_lgth
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 #if $reads.paired == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 #if int($reads.ins_length) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 -ins_length $reads.ins_length
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 #if $reads.options.advanced == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 #if int($reads.options.ins_length_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 -ins_length_sd $reads.options.ins_length_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40 #if int($reads.options.ins_length2) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 -ins_length2 $reads.options.ins_length2
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 #if int($reads.options.ins_length2_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 -ins_length2_sd $reads.options.ins_length2_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 #if int($reads.options.ins_length_long) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 -ins_length_long $reads.options.ins_length_long
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49 #if int($reads.options.ins_length_long_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 -ins_length_long_sd $reads.options.ins_length_long_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 #if int($reads.options.max_branch_length) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 -max_branch_length $reads.options.max_branch_length
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 #end if
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55 #if int($reads.options.max_divergence) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56 -max_divergence $reads.options.max_divergence
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 #if int($reads.options.max_gap_count) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 -max_gap_count $reads.options.max_gap_count
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60 #end if
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61 #if int($reads.options.min_pair_count) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 -min_pair_count $reads.options.min_pair_count
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64 #if int($reads.options.max_coverage) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 -max_coverage $reads.options.max_coverage
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 #end if
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67 #if int($reads.options.long_mult_cutoff) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 -long_mult_cutoff $reads.options.long_mult_cutoff
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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69 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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70 $reads.options.scaffolding
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71 #end if
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72 #end if
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73 </command>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 <inputs>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75 <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 <conditional name="generate_amos">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 <param name="afg" type="select" label="Generate a AMOS.afg file">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 <option value="no">No</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 <option value="yes">Yes</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 <when value="yes"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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83 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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85 <conditional name="unused_reads">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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86 <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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87 <option value="no">No</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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88 <option value="yes">Yes</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
89 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
90 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
91 <when value="yes"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
92 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
93
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
94 <conditional name="last_graph">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
95 <param name="generate_graph" type="select" label="Generate velvet LastGraph file">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
96 <option value="no">No</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
97 <option value="yes">Yes</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
98 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
99 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
100 <when value="yes"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
101 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
102
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
103 <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
104
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
105 <conditional name="coverage">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
106 <param name="cutoff" type="select" label="Coverage cutoff" help="">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
107 <option value="none">None</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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108 <option value="auto">Automatically Determined</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
109 <option value="value">Specify Cutoff Value</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
110 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
111 <when value="none"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
112 <when value="auto"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
113 <when value="value">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
114 <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
115 </when>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
116 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
117
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
118 <conditional name="expected">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
119 <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
120 <option value="none">None</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
121 <option value="auto">Automatically Determined</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
122 <option value="value">Specify Expected Value</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
123 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
124 <when value="none"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
125 <when value="auto"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
126 <when value="value">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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127 <param name="exp_cov" value="10.0" label="Remove nodes with coverage below" type="float" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
128 </when>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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129 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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130
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
131 <conditional name="contig_lgth">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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132 <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
133 <option value="no">No</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
134 <option value="yes">Yes</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
135 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
136 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
137 <when value="yes">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
138 <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
139 </when>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
140 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
141
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
142 <conditional name="reads">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
143 <param name="paired" type="select" label="Using Paired Reads">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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144 <option value="no">No</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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145 <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
146 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
147 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
148 <when value="yes">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
149 <param name="ins_length" value="-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
150 <conditional name="options">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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151 <param name="advanced" type="select" label="Velvet Advanced Options">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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152 <option value="no">Use Defaults</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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153 <option value="yes">Set Advanced Option Values</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
154 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
155 <when value="no"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
156 <when value="yes">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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157 <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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158 <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
159 <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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160 <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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161 <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
162 <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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163 <param name="max_divergence" value="-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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164 <param name="max_gap_count" value="-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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165 <param name="min_pair_count" value="-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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166 <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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167 <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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168 <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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169
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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170 </when>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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171 </conditional>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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172 </when>
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173 </conditional>
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174 </inputs>
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175 <outputs>
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176 <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
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177 <filter>read_trkg is True</filter>
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178 </data>
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179 <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
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180 <filter>last_graph['generate_graph'] == "yes"</filter>
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181 </data>
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182 <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
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183 <filter>generate_amos['afg'] == "yes"</filter>
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184 </data>
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185 <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
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186 <filter>unused_reads['generate_unused'] == "yes"</filter>
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187 </data>
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188 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
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189 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
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190 </outputs>
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191 <requirements>
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192 <requirement type="package">velvet</requirement>
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193 </requirements>
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194 <tests>
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195 <test>
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196 <param name="input" value="velveth_test1/output.html" ftype="velvet" >
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197 <composite_data value='velveth_test1/Sequences' ftype="Sequences"/>
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198 <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/>
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199 <composite_data value='velveth_test1/Log'/>
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200 </param>
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201 <param name="afg" value="yes" />
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202 <param name="generate_unused" value="yes" />
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203 <param name="generate_graph" value="no" />
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204 <param name="read_trkg" value="-read_trkg no" />
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205 <param name="cutoff" value="auto" />
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206 <param name="coverage" value="auto" />
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207 <param name="use_contig_lgth" value="no" />
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208 <param name="paired" value="no" />
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209 <!--
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210 <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/>
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211 -->
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212 <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/>
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213 <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/>
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214 <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/>
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215 <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/>
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216 </test>
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217 </tests>
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218 <help>
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219 **What it does**
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220
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221 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
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222
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223 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
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224
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225 Read the Velvet `documentation`__ for details on using the Velvet Assembler.
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226
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227 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
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228
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229 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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230
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231 ------
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232
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233 **Input formats**
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234
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235 Velvet can input sequence files in the following formats: fasta fastq fasta.gz fastq.gz eland gerald
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236
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237 The input files are prepared for the velvet assembler using **velveth**.
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238
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239 ------
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240
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241 **Outputs**
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242
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243 **Contigs**
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244
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245 The *contigs.fa* file.
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246 This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig length threshold, then the contigs shorter than that value are omitted.
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247 Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
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248 The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
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249
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250 **Stats**
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251
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252 The *stats.txt* file.
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253 This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
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254 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
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255 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
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256 Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.
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257
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258 **LastGraph**
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259
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260 The *LastGraph* file.
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261 This file describes in its entirety the graph produced by Velvet.
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262
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263 **AMOS.afg**
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264
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265 The *velvet_asm.afg* file.
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266 This file is mainly designed to be read by the open-source AMOS genome assembly package. Nonetheless, a number of programs are available to transform this kind of file into other assembly file formats (namely ACE, TIGR, Arachne and Celera). See http://amos.sourceforge.net/ for more information.
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267 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).
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268
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269 ------
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270
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271 **Velvet parameter list**
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272
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273 This is a list of implemented Velvetg options::
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274
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275 Standard options:
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276 -cov_cutoff floating-point|auto : removal of low coverage nodes AFTER tour bus or allow the system to infer it
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277 (default: no removal)
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278 -ins_length integer : expected distance between two paired end reads (default: no read pairing)
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279 -read_trkg yes|no : tracking of short read positions in assembly (default: no tracking)
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280 -min_contig_lgth integer : minimum contig length exported to contigs.fa file (default: hash length * 2)
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281 -amos_file yes|no : export assembly to AMOS file (default: no export)
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282 -exp_cov floating point|auto : expected coverage of unique regions or allow the system to infer it
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283 (default: no long or paired-end read resolution)
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284
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285 Advanced options:
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286 -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
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287 -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing)
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288 -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length)
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289 [replace '*' by nothing, '2' or '_long' as necessary]
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290 -scaffolding yes|no : scaffolding of contigs used paired end information (default: on)
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291 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
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292 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
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293 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
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294 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
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295 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
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296 -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2)
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297 -unused_reads yes|no : export unused reads in UnusedReads.fa file (default: no)
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298
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299 Output:
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300 directory/contigs.fa : fasta file of contigs longer than twice hash length
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301 directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff
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302 directory/LastGraph : special formatted file with all the information on the final graph
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303 directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
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304
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305 </help>
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306 <expand macro="citation"/>
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307 </tool>