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1 <tool id="blockclust" name="BlockClust" version="0.1">
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2 <description>Non-coding RNA clustering from deep sequencing read profiles</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">blockclust</requirement>
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5
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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6 <requirement type="package" version="0.1.19 ">samtools</requirement>
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7 <requirement type="R-module">ggplot2</requirement>
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8 <requirement type="R-module">ape</requirement>
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9
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9 <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement>
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4
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10 </requirements>
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11 <!--<version_command> -version</version_command>-->
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12 <command>
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12
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13 #if str($tool_mode.operation) == "pre":
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4
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14 #set $outputdir = $tags_bed.extra_files_path
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12
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15 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed;
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4
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16 #end if
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17
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12
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18 #if str($tool_mode.operation) == "clust":
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19 #set $outputdir = $clusters.extra_files_path
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20 #set $accept_bed=list()
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21 #set $reject_bed=list()
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22 ## prepare annotations
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12
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23 #if str($tool_mode.reference) == "hg19":
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24 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
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25 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
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12
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26 #elif str($tool_mode.reference) == "mm10":
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27 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
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28 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
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12
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29 #elif str($tool_mode.reference) == "dm3":
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30 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
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31 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
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32 #end if
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33 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
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12
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34 -t $tool_mode.input_bbo
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35 -a #echo ''.join( $accept_bed )
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36 -r #echo ''.join( $reject_bed )
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12
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37 -o $outputdir
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38 #if str($tool_mode.pred.enable_pred) == "yes":
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39 -p
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40 -pm $tool_mode.pred.pred_mode
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41 -md \$BLOCKCLUST_DATA_PATH/models
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42 -x 3;
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43 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
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44 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
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45 #elif str($tool_mode.pred.pred_mode) == "model_based":
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46 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
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47 #end if
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48 #else:
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49 ;
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50 #end if
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51
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52 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
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53 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
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54 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
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55 #end if
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56
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12
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57 #if str($tool_mode.operation) == "post":
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58 #set $outputdir = $clusters_bed.extra_files_path
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59 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
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60 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
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61 #end if
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62 </command>
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63 <inputs>
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64 <conditional name="tool_mode">
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65 <param name="operation" type="select" label="Select mode of operation">
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66 <option value="pre">Pre-processing </option>
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67 <option value="clust">Clustering</option>
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68 <option value="post">Post-processing</option>
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69 </param>
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70 <when value="pre">
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71 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
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72 </when>
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73 <when value="clust">
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74 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
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75 <param name="reference" type="select" label="Select reference genome">
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76 <option value="hg19">Human (hg19)</option>
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77 <option value="mm10">Mouse (mm10)</option>
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78 <option value="dm3">Fly (dm3)</option>
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79 </param>
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80 <conditional name="pred">
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81 <param name="enable_pred" type="select" label="Would you like to perform classification?">
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82 <option value="no">No</option>
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83 <option value="yes">Yes</option>
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84 </param>
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85 <when value="yes">
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86 <param name="pred_mode" type="select" label="Mode of classification">
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87 <option value="model_based">Model based</option>
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88 <option value="nearest_neighbour">Nearest neighbour</option>
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89 </param>
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90 </when>
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91 </conditional>
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92 </when>
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93 <when value="post">
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94 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
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95 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
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96 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
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97 </when>
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98 </conditional>
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99 </inputs>
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100
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101 <outputs>
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102 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
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103 <filter> tool_mode["operation"]=="pre"</filter>
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104 </data>
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105 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
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106 <filter> tool_mode["operation"]=="clust"</filter>
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107 </data>
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108 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
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109 <filter> tool_mode["operation"]=="clust"</filter>
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110 </data>
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111 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}">
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112 <filter>
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113 ((
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114 tool_mode["operation"] == 'clust' and
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115 tool_mode["pred"]["enable_pred"] == "yes" and
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116 tool_mode["pred"]["pred_mode"] == "model_based"
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117 ))
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118 </filter>
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119 </data>
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120 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}">
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121 <filter>
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122 ((
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123 tool_mode["operation"] == 'clust' and
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124 tool_mode["pred"]["enable_pred"] == "yes" and
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125 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
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126 ))
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127 </filter>
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128 </data>
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129 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
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130 <filter> tool_mode["operation"]=="clust"</filter>
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131 </data>
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132 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" >
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133 <filter> tool_mode["operation"]=="post"</filter>
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134 </data>
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135 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
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136 <filter> tool_mode["operation"]=="post"</filter>
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137 </data>
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138 </outputs>
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139 <help>
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140
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141 .. class:: infomark
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142
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143 **What it does**
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144
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145 Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.
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146
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147 **Inputs**
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148
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149 BlockClust needs output of tool blockbuster as input
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150
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151 **Output**
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152
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153 BlockClust produces a fasta file containing clusters.
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154
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155 ------
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156
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157 **Licenses**
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158
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159 If **BlockClust** is used to obtain results for scientific publications it
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160 should be cited as [1]_.
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161
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162 **References**
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163
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164 .. [1]
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165
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166
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167 </help>
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168 </tool>
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