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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:52:16 -0400
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4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="velvetg_jgi" name="velvetg" version="1.0.0">
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2 <description>Assemble preprocessed reads</description>
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3 <command interpreter='perl'>velvetg_jgi_wrapper.pl
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4 $velveth.extra_files_path
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5 $velvetg_outfile.extra_files_path
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6 $velvetg_outfile
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7 $contigs_outfile
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8 $stats_outfile
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9 $lastgraph_outfile
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10 $unused_reads_outfile
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11 $amos_outfile
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12 velvetg $velvetg_outfile.extra_files_path
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13 -very_clean yes
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14 #if $ins_length != '':
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15 -ins_length $ins_length
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16 #if $ins_length_sd != '':
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17 -ins_length_sd $ins_length_sd
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18 #end if
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19 #end if
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 #if $ins_length2 != '':
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 -ins_length2 $ins_length2
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22 #if $ins_length2_sd != '':
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 -ins_length2_sd $ins_length2_sd
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24 #end if
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25 #end if
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26 #if $ins_length3 != '':
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27 -ins_length3 $ins_length3
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28 #if $ins_length3_sd != '':
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29 -ins_length3_sd $ins_length3_sd
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30 #end if
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31 #end if
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32 #if $ins_length4 != '':
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33 -ins_length4 $ins_length4
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34 #if $ins_length4_sd != '':
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35 -ins_length4_sd $ins_length4_sd
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36 #end if
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37 #end if
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38 #if $ins_length5 != '':
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39 -ins_length5 $ins_length5
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40 #if $ins_length5_sd != '':
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41 -ins_length5_sd $ins_length5_sd
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42 #end if
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43 #end if
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44 #if $ins_length_long != '':
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45 -ins_length_long $ins_length_long
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46 #if $ins_length_long_sd != '':
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47 -ins_length_long_sd $ins_length_long_sd
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48 #end if
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49 #end if
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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50 -exp_cov $exp_cov
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51 -cov_cutoff $cov_cutoff
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52 -long_cov_cutoff $long_cov_cutoff
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53 -max_coverage $max_coverage
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54 -min_contig_lgth $min_contig_lgth
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55 -read_trkg $read_trkg
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56 -amos_file $amos_file
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57 -unused_reads $unused_reads
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58 -max_branch_length $max_branch_length
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59 -max_divergence $max_divergence
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60 -max_gap_count $max_gap_count
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61 -scaffolding $scaffolding
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62 -long_mult_cutoff $long_mult_cutoff
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63 -min_pair_count $min_pair_count
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64 -alignments $alignments
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65 -exportFiltered $exportFiltered
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66 </command>
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67 <inputs>
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68 <param name="velveth" type="data" format="velveth" label="velvet hash"/>
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69
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70 <param name="ins_length" type="text" value='auto' label="[-ins_length] Insert length (bp) of short library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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71 <param name="ins_length_sd" type="text" value='auto' label="[ins_length_sd] Insert length standard deviation (bp) of short library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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72 <param name="ins_length2" type="text" value='auto' label="[ins_length2] Insert length (bp) of short2 library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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73 <param name="ins_length2_sd" type="text" value='auto' label="[-ins_length2_sd] Insert length standard deviation (bp) of short2 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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74 <param name="ins_length3" type="text" value='auto' label="[ins_length3] Insert length (bp) of short3 library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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75 <param name="ins_length3_sd" type="text" value='auto' label="[-ins_length3_sd] Insert length standard deviation (bp) of short3 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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76 <param name="ins_length4" type="text" value='auto' label="[ins_length4] Insert length (bp) of short4 library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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77 <param name="ins_length4_sd" type="text" value='auto' label="[-ins_length4_sd] Insert length standard deviation (bp) of short4 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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78 <param name="ins_length5" type="text" value='auto' label="[ins_length5] Insert length (bp) of short5 library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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79 <param name="ins_length5_sd" type="text" value='auto' label="[-ins_length5_sd] Insert length standard deviation (bp) of short5 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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80 <param name="ins_length_long" type="text" value='auto' label="[ins_length_long] Insert length (bp) of long library" help="blank=no read pairing; auto=infer; or supply value (integer)" />
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81 <param name="ins_length_long_sd" type="text" value='auto' label="[-ins_length_sd_long] Insert length standard deviation (bp) of long library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" />
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82
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83 <param name='exp_cov' type='text' value='-1' label='[-exp_cov] Expected short read k-mer coverage' help='-1=no long or paired-end read resolution; auto=infer it; or supply value (real number)' />
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84 <param name="cov_cutoff" type="text" value='-1' label="[-cov_cutoff] Removal of low coverage nodes AFTER tour bus" help="-1=no removal; auto=infer cutoff; or specify cutoff (real number)" />
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85 <param name="long_cov_cutoff" type="float" value='-1' label="[-long_cov_cutoff] Removal of low long-read coverage nodes AFTER tour bus" help="-1=no removal; or specify cutoff (real number)" />
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86 <param name='max_coverage' type='float' value='-1' label="[-max_coverage] Exclude highly covered data from your assembly (e.g. plasmid, mitochondrial, and chloroplast sequences)" help='-1 for default: no removal' />
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87 <param name="min_contig_lgth" type="integer" value='-1' label="Minimum contig length" help="-1 for default: hash length *2" />
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88 <param name="scaffolding" type="boolean" checked='true' label="Scaffolding" truevalue='yes' falsevalue='no'/>
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89
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90 <!-- Tour Bus Parameters -->
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91 <param name="max_branch_length" type="integer" value='100' label="Maximum branch length" help="Default recommended"/>
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92 <param name="max_divergence" type="float" value='0.20' label="Maximum divergence rate" help="Default recommended"/>
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93 <param name="max_gap_count" type="integer" value='3' label="Maximum gap count" help="Default recommended"/>
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94
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95 <!-- Rock Band Parameters -->
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96 <param name='long_mult_cutoff' type="integer" value='2' label="Minimum long read connection cutoff"/>
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97
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98 <!-- Pebble Parameters -->
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99 <param name="min_pair_count" type="integer" value='10' label="Minimum Read-Pair Validation"/>
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100
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101 <!-- Output Parameters -->
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102 <param name='unused_reads' type='boolean' truevalue='yes' falsevalue='no' checked='true' label='Export unused reads' />
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103 <param name='read_trkg' type='boolean' truevalue='yes' falsevalue='no' checked='false' label="[-read_trkg] tracking of short read positions in assembly" help="This will cost slightly more memory and calculation time, but will have the advantage of producing in the end a more detailed description of the assembly. The additional information will be included in the LastGraph file and optionally the Amos assembly file (below)." />
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104 <param name='amos_file' type='boolean' truevalue='yes' falsevalue='no' checked='false' label="[-amos_file] export assembly to AMOS file" help="If selecting this option, you may also want to select -read_trkg (above)" />
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105 <param name="alignments" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-alignments] export a summary of contig alignment to the reference sequences" />
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106 <param name="exportFiltered" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-exportFiltered] export the long nodes which were eliminated by the coverage filters" />
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107 </inputs>
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108
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109 <outputs>
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110 <data name="velvetg_outfile" format="txt" />
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111 <data name="contigs_outfile" format="fasta" label='Contigs' />
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112 <data name="stats_outfile" format="tabular" label='Contig Stats' />
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113 <data name="lastgraph_outfile" format="txt" label="LastGraph" />
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114 <data name='unused_reads_outfile' format='fasta' label='Unused Reads'>
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115 <filter>unused_reads is True</filter>
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116 </data>
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117 <data name='amos_outfile' format='txt' label='Amos Assembly'>
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118 <filter>amos_file is True</filter>
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119 </data>
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120 </outputs>
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121
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122 <help>
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123
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124 **What it does**
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125
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126 This tool assembles contigous sequences from preprocessed reads by constructing a de Bruijn graph.
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127
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128 Sequences must be preprocessed by the velveth tool.
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129
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130 **Manual**
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131
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132 http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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133 </help>
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134 </tool>