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1 <tool id="ctat_lncrna" name="ctat_lncrna" version="1.0.0" profile="17.05">
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2
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3 <description>Filters a high-quality set of lncRNA from reconstructed RNA-seq data</description>
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4 <requirements>
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5 <requirement type="package">ctat-lncrna</requirement>
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6 </requirements>
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7 <command detect_errors="default">
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8 <![CDATA[
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9 #if str($bedfile) != "":
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10 lncrna --bedfile $bedfile
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9
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11 --config "${assembly.fields.path}"
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0
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12 #end if
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13
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14 #if str($assembly) != "":
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9
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15 --assembly "${assembly.fields.value}"
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0
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16 #end if
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17
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18 #if $min_overlap != "":
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19 --min_overlap "$min_overlap"
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20 #end if
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21
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22 #if str($min_cluster) != "":
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23 --min_cluster "$min_cluster"
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24 #end if
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25
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26 #if str($min_coding) != "":
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27 --min_coding "$min_coding"
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28 #end if
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29
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30 #if str($minMatch) != "":
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31 --minMatch "$minMatch"
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32 #end if
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33
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34 #if str($pad) != "":
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35 --pad "$pad"
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36 #end if
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37
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38 #if str($gap_open) != "":
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39 --gap_open "$gap_open"
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40 #end if
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41
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42 #if str($gap_extend) != "":
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43 --gap_extend "$gap_extend"
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44 #end if
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45
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46 --web
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47 && cp -r slncky.EvolutionBrowser $html_file.files_path
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48 ]]>
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49 </command>
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50
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51 <inputs>
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52 <param name="bedfile" format="interval" type="data" value="bedfile" label="Bed File:" help="Reconstructed transcripts (ex. from StringTie or Trinity)"/>
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53 <param name="min_overlap" type="float" value="0.0" label="Min overlap" help="Remove any transcript that overlap annotated coding gene greater than min_overlap" />
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54 <param name="min_cluster" type="integer" value="2" label="Min cluster" help="Minimum size of duplication clusters to remove" />
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55 <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/>
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56 <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" />
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57 <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" />
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1
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58 <param name="gap_open" type="text" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/>
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59 <param name="gap_extend" type="text" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/>
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9
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60 <param name="assembly" type="select" label="Choose annotation:" help="Select annotation">
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61 <options from_data_table="ctat_lncrna_annotations" />
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62 </param>
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63 </inputs>
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64
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65 <outputs>
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66 <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/>
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1
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67 <data format="text" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/>
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68 <data format="text" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/>
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69 <data format="text" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/>
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70 <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/>
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1
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71 <data format="text" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/>
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72 <data format="text" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/>
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73 <data format="text" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/>
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74 <data format="text" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/>
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75 </outputs>
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76
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77 <stdio>
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78 <exit_code range="1:" level="fatal" description="Error in SLNCky" />
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79 </stdio>
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80
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81 <tests>
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82 <test>
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83 <param name="bedfile" value="reads.simPE.StringTie.transcripts.bed" />
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84 <param name="assembly" value="hg19" />
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85 <param name="min_overlap" value="0.0" />
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86 <param name="min_cluster" value="2" />
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87 <param name="min_coding" value="0.1" />
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88 <param name="minMatch" value="0.1" />
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89 <param name="pad" value="0" />
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90 <param name="gap_open" value="200" />
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91 <param name="gap_extend" value="40" />
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92
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93 <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
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94 <output name="html_file" file="slncky/reads.simPE.browse.html" />
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95
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96 <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
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97 <output name="canonical_to_lncs" file="slncky/reads.simPE.canonical_to_lncs.txt" />
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98
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99 <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
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100 <output name="cluster_info" file="slncky/reads.simPE.cluster_info.txt" />
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101
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102 <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
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103 <output name="filtered_info" file="slncky/reads.simPE.filtered_info.txt" />
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104
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105 <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
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106 <output name="lncs" file="slncky/reads.simPE.lncs.bed" />
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107
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108 <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
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109 <output name="lncs_info" file="slncky/reads.simPE.lncs.info.txt" />
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110
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111 <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
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112 <output name="orfs" file="slncky/reads.simPE.orfs.txt" />
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113
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114 <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
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115 <output name="orthologs_top" file="slncky/reads.simPE.orthologs.top.txt" />
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116
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117 <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
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118 <output name="orthologs" file="slncky/reads.simPE.orthologs.txt" />
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119
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120 </test>
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121 <test>
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122 <param name="bedfile" value="mir-17-92.StringTie.transcripts.bed" />
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123 <param name="assembly" value="hg19" />
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124 <param name="min_overlap" value="0.0" />
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125 <param name="min_cluster" value="2" />
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126 <param name="min_coding" value="0.1" />
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127 <param name="minMatch" value="0.1" />
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128 <param name="pad" value="0" />
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129 <param name="gap_open" value="200" />
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130 <param name="gap_extend" value="40" />
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131
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132 <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
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133 <output name="html_file" file="slncky/mir-17-92.browse.html" />
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134
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135 <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
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136 <output name="canonical_to_lncs" file="slncky/mir-17-92.canonical_to_lncs.txt.sorted" sort="true" />
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137
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138 <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
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139 <!-- This file isn't being created for some reason...
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140 <output name="cluster_info" >
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141 <assert_contents>
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142 <has_line_matching expression=".+" />
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143 </assert_contents>
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144 </output>
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145 -->
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146
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147 <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
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148 <output name="filtered_info" file="slncky/mir-17-92.filtered_info.txt.sorted" sort="true" />
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149
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150 <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
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151 <output name="lncs" file="slncky/mir-17-92.lncs.bed" />
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152
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153 <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
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154 <output name="lncs_info" file="slncky/mir-17-92.lncs.info.txt" />
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155
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156 <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
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157 <output name="orfs" file="slncky/mir-17-92.orfs.txt" />
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158
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159 <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
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160 <output name="orthologs_top" file="slncky/mir-17-92.orthologs.top.txt" />
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161
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162 <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
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163 <output name="orthologs" file="slncky/mir-17-92.orthologs.txt" />
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164 </test>
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165 </tests>
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166
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167 <help>
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168 .. class:: infomark
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169
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170 slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.
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171
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172 To learn more about slncky read their paper_ or visit their website_ .
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173
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174 .. _paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0880-9
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175 .. _website: https://github.com/slncky/slncky
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176
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177 </help>
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178 </tool>
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