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1 <tool id="tapdance_runner" name="TAPDANCE" version="1.0" force_history_refresh="True">
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2 <description>A tool for identifying Common Insertion Sites</description>
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3 <command interpreter="perl">tapdance_runner.pl -index $index -index_id $index.id -index_path $index.extra_files_path
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4 #if $predef.predef_select.__str__() == 'PREDEF':
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5 -s $predef.seqs -b $predef.bar2lib -pn $userEmail$predef.proj_name -config $predef.config
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6 #else
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7 ## INPUT
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8 #if $predef.start_point.start_select.__str__() == 'sequences':
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9 -s $predef.start_point.seqs -b $predef.start_point.bar2lib -bowtieIdx $predef.start_point.genomeIdx -pn $userEmail$predef.start_point.proj_name
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10 #for $entry in $predef.start_point.mutagens
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11 #if $entry.mutagen.mutagen_select.__str__() == 'CUSTOM':
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12 -mutagen $entry.mutagen.mutagen_custom.__str__()
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13 #else
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14 -mutagen $entry.mutagen.mutagen_select.__str__()
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15 #end if
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16 #end for
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17 #end if
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18 #if $predef.start_point.start_select.__str__() == 'single_project':
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19 -pn $predef.start_point.cis_project.__str__()
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20 #end if
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21 #if $predef.start_point.start_select.__str__() == 'multiple_projects':
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22 -pn $userEmail$predef.start_point.proj_name -merge $predef.start_point.merge_projects.__str__()
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23 #end if
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24
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25 ## OUTPUT
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26 #if $predef.start_point.start_select.__str__() != 'single_project':
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27 -pb $projBed -projectBedId $projBed.id
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28 ##-ps $projSum -projectSummaryId $projSum.id -pv $projVis -projectVisId $projVis.id
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29 #end if
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30 #if $predef.results.result_select.__str__() == 'cis':
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31 -cw $cisWig -cwid $cisWig.id -cwpath $__new_file_path__
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32 ##-cs $cisSum -cisSumId $cisSum.id
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33 -lib_pct $predef.results.cis_params.lib_pct -CIS_tot_p $predef.results.cis_params.CIS_tot_p -CIS_lib_p $predef.results.cis_params.CIS_lib_p -CIS_reg_p $predef.results.cis_params.CIS_reg_p -coCIS_thresh $predef.results.cis_params.coCIS_thresh
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34 #if $predef.results.metadata.metadata_select.__str__() == 'CUSTOM':
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35 -m $predef.results.metadata.metadata_custom.__str__()
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36 #end if
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37 #if $predef.results.annotation.annotation_select.__str__() == 'CUSTOM':
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38 -m $predef.results.annotation.annotation_file.__str__()
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39 #end if
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40 #for $entry in $predef.results.omitChroms
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41 -o $entry.omitChrom.__str__()
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42 #end for
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43 #else
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44 -no_cis
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45 #end if
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46 #end if
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47 </command>
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48 <inputs>
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49 <conditional name="predef">
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50 <param name="predef_select" type="select" label="Enter values below or use a predefined config file?">
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51 <option value="CUSTOM">Enter values below</option>
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52 <option value="PREDEF">Use predefined config file</option>
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53 </param>
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54 <when value="PREDEF">
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55 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
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56 <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
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57 <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
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58 <param name="config" type="data" format="text" label="Predefined Config File" optional="false"/>
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59 <conditional name="metadata">
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60 <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
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61 <option value="AUTOMATIC">Generate default</option>
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62 <option value="CUSTOM">Use uploaded data</option>
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63 </param>
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64 <when value="AUTOMATIC">
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65 <param name="metadata_custom" type="hidden" value=""/>
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66 </when>
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67 <when value="CUSTOM">
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68 <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
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69 </when>
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70 </conditional>
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71 </when>
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72 <when value="CUSTOM">
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73 <conditional name="start_point">
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74 <param name="start_select" type="select" label="Starting Point">
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75 <option value="sequences">FASTQ or FASTA</option>
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76 <option value="single_project">Existing Project</option>
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77 <option value="multiple_projects">Merge Multiple Projects</option>
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78 </param>
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79 <when value="sequences">
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80 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
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81 <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/>
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82 <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/>
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83 <repeat name="mutagens" title="Mutagen(s)" min="1">
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84 <conditional name="mutagen">
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85 <param name="mutagen_select" type="select" label="Mutagen matching" help="Choose the appropriate match for this experiment">
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86 <option value="TGTATGTAAACTTCCGACTTCAACTG">Sleeping Beauty Example, TGTATGTAAACTTCCGACTTCAACTG</option>
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87 <option value="CUSTOM">Other</option>
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88 </param>
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89 <when value="TGTATGTAAACTTCCGACTTCAACTG">
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90 <param name="mutagen_custom" type="hidden" value=""/>
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91 </when>
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92 <when value="CUSTOM">
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93 <param name="mutagen_custom" type="text" label="Mutagen Sequence" help="Enter the sequence to match as the mutagen, '_' may be used to match any single base. E.G. _GTATGTAAACTTCCGACTTCAACTG would match both AGTATGTAAACTTCCGACTTCAACTG and TGTATGTAAACTTCCGACTTCAACTG"/>
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94 </when>
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95 </conditional>
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96 </repeat>
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97 <param name="genomeIdx" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact help@msi.umn.edu">
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98 <options from_file="bowtie_indices.loc">
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99 <column name="value" index="3" />
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100 <column name="name" index="0" />
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101 </options>
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102 </param>
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103 </when>
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104 <when value="single_project">
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105 <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
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106 <param name="cis_project" type="select" label="Project" data_ref="proj_source">
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107 <options from_dataset="proj_source">
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108 <column name="name" index="1"/>
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109 <column name="value" index="0"/>
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110 </options>
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111 </param>
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112 </when>
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113 <when value="multiple_projects">
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114 <param name="proj_name" type="text" label="New Project Name" optional="false"/>
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115 <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/>
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116 <param name="merge_projects" type="select" multiple="true" label="Projects to Merge" data_ref="proj_source">
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117 <options from_dataset="proj_source">
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118 <column name="name" index="1"/>
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119 <column name="value" index="0"/>
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120 </options>
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121 </param>
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122 </when>
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123 </conditional>
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124 <conditional name="results">
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125 <param name="result_select" type="select" label="Desired Results">
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126 <option value="cis">CIS calls</option>
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127 <option value="inserts">Inserts Only (useful for QC)</option>
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128 </param>
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129 <when value="inserts">
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130 <param type="hidden" value="" name="inserts_only"/>
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131 </when>
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132 <when value="cis">
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133 <conditional name="metadata">
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134 <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom">
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135 <option value="AUTOMATIC">Generate default</option>
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136 <option value="CUSTOM">Use uploaded data</option>
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137 </param>
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138 <when value="AUTOMATIC">
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139 <param name="metadata_custom" type="hidden" value=""/>
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140 </when>
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141 <when value="CUSTOM">
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142 <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/>
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143 </when>
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144 </conditional>
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145 <repeat name="omitChroms" title="Chromosomes to Omit" help="The chromosome of the donor concatemer is often omitted">
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146 <param type="text" name="omitChrom" label="Chromosome Label" help="e.g. chr1"/>
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147 </repeat>
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148 <conditional name="annotation">
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149 <param name="annotation_select" label="Annotation Features" type="select" help="Specify an interval file containing genomic features to annotate CIS calls">
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150 <option value="DEFAULT">Default: mm9 refSeq genes</option>
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151 <option value="CUSTOM">Specify interval file</option>
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152 </param>
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153 <when value="DEFAULT">
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154 <param type="hidden" name="annotation_file" value=""/>
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155 </when>
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156 <when value="CUSTOM">
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157 <param type="data" format="interval" name="annotation_file" label="Annotation Source"/>
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158 </when>
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159 </conditional>
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160 <conditional name="cis_params">
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161 <param name="cis_params_select" type="select" label="CIS calling parameters">
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162 <option value="default">Use defaults</option>
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163 <option value="custom">Specify values</option>
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164 </param>
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165 <when value="default">
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166 <param type="hidden" value="0.0001" name="lib_pct"/>
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167 <param type="hidden" value="0.05" name="CIS_tot_p"/>
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168 <param type="hidden" value="0.05" name="CIS_lib_p"/>
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169 <param type="hidden" value="0.05" name="CIS_reg_p"/>
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170 <param type="hidden" value="0.0001" name="coCIS_thresh"/>
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171 </when>
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172 <when value="custom">
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173 <param type="float" value="0.0001" name="lib_pct" label="Library Percent"/>
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174 <param type="float" value="0.05" name="CIS_tot_p" label="CIS Total pvalue"/>
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175 <param type="float" value="0.05" name="CIS_lib_p" label="CIS Library pvalue"/>
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176 <param type="float" value="0.05" name="CIS_reg_p" label="CIS Region pvalue"/>
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177 <param type="float" value="0.0001" name="coCIS_thresh" label="coCIS Threshold"/>
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178 </when>
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179 </conditional>
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180 </when>
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181 </conditional>
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182 </when>
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183 </conditional>
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184 </inputs>
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185 <outputs>
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186 <data format="html" name="index" label="TAPDANCE Results"/>
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187 <data format="bed" name="projBed" label="Non Redundant Inserts BED" visible="false">
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188 <filter>(
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189 predef['predef_select'] == 'PREDEF' or
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190 predef['start_point']['start_select'] != 'single_project'
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191 )
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192 </filter>
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193 </data>
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194 <!--
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195 <data format="txt" name="projSum" label="Summary" hidden="true">
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196 <filter>(
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197 predef['predef_select'] == 'PREDEF' or
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198 predef['start_point']['start_select'] == 'sequences'
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199 )
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200 </filter>
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201 </data>
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202 <data format="pdf" name="projVis" label="Insert Graphs">
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203 <filter>(predef['predef_select'] == 'PREDEF' or predef['start_point']['start_select'] != 'single_project')</filter>
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204 </data>
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205 -->
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206 <!-- due to optional start with seqs, can no longer use the seqs metadata as a source for cisWig metadata -->
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207 <data format="wig" name="cisWig" label="CIS WIG">
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208 <filter>(
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209 predef['predef_select'] == 'PREDEF' or
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210 predef['results']['result_select'] == 'cis'
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211 )
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212 </filter>
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213 </data>
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214 <!--
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215 <data format="txt" name="cisSum" label="CIS Summary">
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216 <filter>(
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217 predef['predef_select'] == 'PREDEF' or
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218 predef['results']['result_select'] == 'cis'
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219 )
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220 </filter>
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221 </data>
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222 -->
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223 </outputs>
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224 <!--<code file="tapdance_index.py">
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225 <hook exec_after_process="exec_after_completion" />
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226 </code>-->
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227 <help>
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228 See full help at https://sourceforge.net/p/tapdancebio/wiki/
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229
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230 `Report a Problem`_
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231
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232 .. _Report a Problem: https://sourceforge.net/p/tapdancebio/tickets/new/
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233
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234 </help>
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235 </tool>
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