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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 <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 </requirements>
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10 <!--<version_command> -version</version_command>-->
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11 <command>
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12 #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
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13
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14 #if str($mode.operation) == "pre":
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15 #set $outputdir = $tags_bed.extra_files_path
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16 BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
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17 #end if
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18
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19 #if str($mode.operation) == "clust":
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20 #set $outputdir = $clusters.extra_files_path
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21 #set $accept_bed=list()
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22 #set $reject_bed=list()
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23 ## prepare annotations
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24 #if str($mode.reference) == "hg19":
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25 $accept_bed.append("$blockclust_data_path/annotations/hg19/hg19.accept.bed")
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26 $reject_bed.append("$blockclust_data_path/annotations/hg19/hg19.reject.bed")
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27 #elif str($mode.reference) == "mm10":
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28 $accept_bed.append("$blockclust_data_path/annotations/mm10/mm10.accept.bed")
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29 $reject_bed.append("$blockclust_data_path/annotations/mm10/mm10.reject.bed")
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30 #elif str($mode.reference) == "dm3":
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31 $accept_bed.append("$blockclust_data_path/annotations/dm3/dm3.accept.bed")
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32 $reject_bed.append("$blockclust_data_path/annotations/dm3/dm3.reject.bed")
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33 #end if
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34 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c $blockclust_data_path/blockclust.config
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35 -t $mode.input_bbo
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36 -a #echo ''.join( $accept_bed )
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37 -r #echo ''.join( $reject_bed )
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38 -o $outputdir;
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39 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
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40 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
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41 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
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42 #end if
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43
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44 #if str($mode.operation) == "post":
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45 #set $outputdir = $clusters_bed.extra_files_path
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46 BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam $blockclust_data_path/rfam_map.txt;
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47 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
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48 #end if
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49 </command>
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50 <inputs>
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51 <conditional name="mode">
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52 <param name="operation" type="select" label="Select mode of operation">
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53 <option value="pre">Pre-processing </option>
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54 <option value="clust">Clustering</option>
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55 <option value="post">Post-processing</option>
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56 </param>
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57 <when value="pre">
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58 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
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59 </when>
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60 <when value="clust">
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61 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
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62 <param name="reference" type="select" label="Select reference genome">
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63 <option value="hg19">Human (hg19)</option>
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64 <option value="mm10">Mouse (mm10)</option>
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65 <option value="dm3">Fly (dm3)</option>
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66 </param>
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67 </when>
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68 <when value="post">
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69 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
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70 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
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71 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
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72 </when>
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73 </conditional>
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74 </inputs>
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75
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76 <outputs>
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77 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
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78 <filter> mode["operation"]=="pre"</filter>
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79 </data>
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80 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
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81 <filter> mode["operation"]=="clust"</filter>
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82 </data>
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83 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
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84 <filter> mode["operation"]=="clust"</filter>
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85 </data>
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86 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
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87 <filter> mode["operation"]=="clust"</filter>
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88 </data>
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89 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" >
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90 <filter> mode["operation"]=="post"</filter>
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91 </data>
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92 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
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93 <filter> mode["operation"]=="post"</filter>
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94 </data>
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95 </outputs>
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96 <help>
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97
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98 .. class:: infomark
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99
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100 **What it does**
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101
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102 Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.
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103
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104 **Inputs**
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105
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106 BlockClust needs output of tool blockbuster as input
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107
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108 **Output**
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109
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110 BlockClust produces a fasta file containing clusters.
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111
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112 ------
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113
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114 **Licenses**
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115
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116 If **BlockClust** is used to obtain results for scientific publications it
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117 should be cited as [1]_.
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118
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119 **References**
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120
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121 .. [1]
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122
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123 ------
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124
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125 </help>
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126 </tool>
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