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annotate spaln.xml @ 1:37b5e1f0b544 draft

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"planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
author iuc
date Thu, 16 Jul 2020 07:57:10 -0400
parents 95ea8d97abb4
children dd0cd2319ae5
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95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
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2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
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3 <macros>
1
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4 <import>macros.xml</import>
0
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5 </macros>
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6 <edam_topics>
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7 <edam_topic>topic_3512</edam_topic>
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8 </edam_topics>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
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11 </requirements>
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12 <command detect_errors="aggressive"><![CDATA[
1
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13 spaln -t\${GALAXY_SLOTS:-1} -O$format
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14 #if str($species_params).strip() != ''
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15 -T'${species_params}'
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16 #end if
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17 #if $adv.use == "yes"
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18 -S'${adv.query_orientation}'
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19 -V'${adv.hirschberg_threshold}'
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20 -pa'${adv.polya_trim}'
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21 ${adv.all_results}
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22 -yu'${adv.gap_extension_penalty}'
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23 -yv'${adv.gap_open_penalty}'
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24 -yw'${adv.dp_matrix_scan_width}'
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25 -ya'${adv.splice_stringency}'
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26 -yj'${adv.gap_penalty_incline}'
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27 -yk'${adv.gap_penalty_flex}'
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28 '${adv.double_affine_gap}'
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29 -ym'${adv.match_score}'
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30 -yn'${adv.mismatch_score}'
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31 -yo'${adv.stop_codon_penalty}'
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32 -yx'${adv.frameshift_penalty}'
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33 -yy'${adv.splice_site_weight}
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34 -yz'${adv.coding_potential_weight}'
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35 -yB'${adv.branch_point_weight}
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36 -yL'${adv.min_intron_len}'
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37 -yZ'${adv.intron_potential_weight}'
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38 #if str($adv.max_gene_length).strip() != ''
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39 -XG'${adv.max_gene_length}'
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40 #end if
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41 #end if
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42 '$genome' '$query' >'$output1'
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43 ]]></command>
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44 <inputs>
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45 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
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46 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
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47 <param argument="-O" type="select" name="format" label="Output format">
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48 <option value="0">GFF3 format genes</option>
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49 <option value="2">GFF3 format matches</option>
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50 <option value="3">BED format</option>
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51 <option value="4">Tabular format exon information</option>
1
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52 </param>
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53 <param argument="-T" name="species_params" type="text" optional="true" label="Species to use for parameter setting" help="Choose a species table (e.g. cynosemi) from which to read parameters to optimise spaln" />
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54 <conditional name="adv">
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55 <param type="select" name="use" label="Advanced settings">
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56 <option selected="true" value="no">No</option>
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57 <option value="yes">Yes</option>
0
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58 </param>
1
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59 <when value="no">
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60 </when>
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61 <when value="yes">
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62 <param argument="-S" name="query_orientation" type="select" label="DNA query orientation" help="Determines how to treat orientation of query sequence when searching">
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63 <option value="0">Infer orientation from sequence header (no poly-A/poly-T trimming)</option>
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64 <option value="1">Forward orientation only. Poly-A tail might be trimmed off</option>
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65 <option value="2">Reverse orientation only. Leading poly-T might be trimmed off</option>
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66 <option selected="true" value="3">Examine both orientations. Poly-A / Poly-T might be trimmed off</option>
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67 </param>
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68 <param argument="-V" name="hirschberg_threshold" type="integer" value="16777216" label="Minimum space to induce Hirschberg's algorithm" help="Default is 16M (16x1024x1024 bytes)" />
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69 <param argument="-pa" name="polya_trim" type="integer" value="12" label="Limit 3' poly-As to this number of bases" help="poly-A/poly-T trimming is only done if -S (orientation) option is 0 or 3" />
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70 <param argument="-pw" name="all_results" type="boolean" checked="false" truevalue="-pw" falsevalue="" label="Report results even if the score is below the threshold" />
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71 <param argument="-yu" name="gap_extension_penalty" type="integer" value="3" label="Gap-extension penalty" />
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72 <param argument="-yv" name="gap_open_penalty" type="integer" value="8" label="Gap-open penalty" />
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73 <param argument="-yw" name="dp_matrix_scan_width" type="integer" value="100" label="Band width for DP matrix scan" />
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74 <param argument="-ya" name="splice_stringency" type="select" label="Stringency of splice site selection" help="Which dinucleotide pairs to accept at the ends of an intron">
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75 <option value="0" selected="true">accept only the canonical pairs (GT..AG,GC..AG,AT..AC)</option>
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76 <option value="1">accept also AT..AN</option>
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77 <option value="2">allow up to one mismatch from GT..AG</option>
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78 <option value="3">accept any pairs</option>
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79 </param>
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80 <param argument="-yj" name="gap_penalty_incline" type="float" value="0.6" label="Incline of long gap penalty" />
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81 <param argument="-yk" name="gap_penalty_flex" type="integer" value="7" label="Flex point where the incline of gap penalty changes" />
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82 <param argument="-yl3" name="double_affine_gap" type="boolean" checked="false" truevalue="-yl3" falsevalue="" label="Use double affine gap penalty" help="Use the double affine gap rathr than single affine gap penalty calculation" />
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83 <param argument="-ym" name="match_score" type="integer" value="2" label="Nucleotide match score" />
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84 <param argument="-yn" name="mismatch_score" type="integer" value="-6" label="Nucleotide mismatch score" />
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85 <param argument="-yo" name="stop_codon_penalty" type="integer" value="100" label="Penalty for a premature termination codon" />
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86 <param argument="-yx" name="frameshift_penalty" type="integer" value="100" label="Penalty for a frame shift error" />
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87 <param argument="-yy" name="splice_site_weight" type="integer" value="8" label="Weight for splice site signal" />
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88 <param argument="-yz" name="coding_potential_weight" type="integer" value="2" label="Weight for coding potential" />
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89 <param argument="-yB" name="branch_point_weight" type="integer" value="0" label="Weight for branch point signal" />
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90 <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" />
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91 <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" />
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92 <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" />
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93 </when>
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94 </conditional>
0
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95 </inputs>
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96 <outputs>
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97 <data name="output1" format="tabular">
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98 <change_format>
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99 <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
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100 <when input="format" value="0" format="gff3" />
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101 <when input="format" value="2" format="gff3" />
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102 <when input="format" value="3" format="bed12" />
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103 <when input="format" value="4" format="tabular" />
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104 </change_format>
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105 <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
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106 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
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107 commented out till that is merged
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108 <actions>
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109 <conditional name="format">
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110 <when value="4">
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111 <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T # - X P DiNuc" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
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112 </when>
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113 </conditional>
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114 </actions>
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115 -->
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116 </data>
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117 </outputs>
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118 <tests>
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119 <test>
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120 <param name="genome" ftype="fasta" value="genome.fasta" />
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121 <param name="query" ftype="fasta" value="query.fasta" />
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122 <param name="format" value="0"/>
1
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123 <conditional name="adv">
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124 <param name="use" value="no" />
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125 </conditional>
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126 <output name="output1" ftype="gff3" value="output1_gff_genes.gff3" />
0
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127 </test>
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128 <test>
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129 <param name="genome" ftype="fasta" value="genome.fasta" />
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130 <param name="query" ftype="fasta" value="query.fasta" />
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131 <param name="format" value="2"/>
1
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132 <conditional name="adv">
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133 <param name="use" value="no" />
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134 </conditional>
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135 <output name="output1" ftype="gff3" value="output1_gff_matches.gff3" />
0
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136 </test>
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137 <test>
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138 <param name="genome" ftype="fasta" value="genome.fasta" />
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139 <param name="query" ftype="fasta" value="query.fasta" />
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140 <param name="format" value="3"/>
1
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141 <conditional name="adv">
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142 <param name="use" value="no" />
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143 </conditional>
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144 <output name="output1" ftype="bed12" value="output1.bed12" />
0
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145 </test>
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146 <test>
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147 <param name="genome" ftype="fasta" value="genome.fasta" />
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148 <param name="query" ftype="fasta" value="query.fasta" />
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149 <param name="format" value="4"/>
1
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150 <conditional name="adv">
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151 <param name="use" value="no" />
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152 </conditional>
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153 <output name="output1" ftype="tabular" value="output1.tabular" />
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154 </test>
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155 <test>
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156 <param name="genome" ftype="fasta" value="genome.fasta" />
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157 <param name="query" ftype="fasta" value="query.fasta" />
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158 <param name="format" value="4"/>
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159 <param name="species_params" value="cynosemi" />
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160 <conditional name="adv">
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161 <param name="use" value="no" />
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162 </conditional>
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163 <output name="output1" ftype="tabular" value="output2.tabular" />
0
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164 </test>
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165 </tests>
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166 <help><![CDATA[
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167 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
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168 protein sequences onto a whole genomic sequence in a single job.
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169
1
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170 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln. This algorithm
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171 takes FASTA format query and genome sequence and finds an alignment of the query (either cDNA or protein)
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diff changeset
172 against the genome.
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diff changeset
173
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174 Spaln optionally takes a species name to use for parameter setting (the "-T" parameter). The
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175 "List spaln parameter tables" (list_spaln_tables) can be used to find a parameter file that is
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diff changeset
176 close (in terms of taxonomic distance) to your species of interest. Use of this setting is recommended.
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177
0
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178
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179 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
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180 ]]></help>
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181 <citations>
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182 <citation type="doi">0.1093/nar/gkn105</citation>
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183 </citations>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
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184 </tool>