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1 <tool id="oncostrip" name="Oncostrip Plot" version="0.9.30">
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2
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3 <description>
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4 Cohort-wide mutation oncostrip from MAF and (optionally) GISTIC data
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5 </description>
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6
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7 <command detect_errors="aggressive">
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8
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9 mkdir outputs;
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10 touch gene_list.txt;
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11 #if $gene_input_type.gene_input_type_selector.value == "other":
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12 echo $gene_input_type.gene > gene_list.txt;
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13 #else:
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14 cat $gene_input_type.gene_file > gene_list.txt;
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15 #end if
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16
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17 Rscript $__tool_directory__/oncostrip_gistic.R
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18 --input_maf $input_maf
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19 --gene_list gene_list.txt
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20 --output_plot $output_plot
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21 #if $include_anno.anno == "use_anno":
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22 --anno $include_anno.anno_file
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23 #end if
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24 #if $sort_by == "anno":
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25 --sort_by anno
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26 #elif $sort_by == "gene":
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27 --sort_by gene
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28 #else:
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29 --sort_by $sort_by
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30 #end if
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31 #if $include_gistic.gistic == "use_gistic":
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32 -gal $include_gistic.file1
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33 -ga $include_gistic.file2
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34 -gd $include_gistic.file3
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35 #end if
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36 ;
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37
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38 </command>
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39
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40 <inputs>
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41 <param type="data" format="maf" name="input_maf" label="MAF File"/>
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42 <conditional name="gene_input_type">
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43 <param name="gene_input_type_selector" type="select" label="Choose how to input genes">
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44 <option value="file" selected="True">Gene File</option>
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45 <option value="other">Other</option>
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46 </param>
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47 <when value="file">
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48 <param name="gene_file" type="data" format="txt" label="Gene File" help="list of genes separated by newlines" />
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49 </when>
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50 <when value="other">
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51 <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
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52 </when>
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53 </conditional>
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54
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55 <param name="sort_by" type="select" label="Sort samples and genes in output?">
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56 <option value="none">No sorting</option>
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57 <option value="gene">Sort genes and patients using mutation frequency</option>
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58 <option value="anno">Sort on annotation, then mutation frequency</option>
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59 </param>
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60
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61 <conditional name="include_anno">
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62 <param name="anno" type="select" display="radio" label="Optional: include annotation information for each sample">
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63 <option value="use_anno" checked="false">Include</option>
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64 <option value="no_anno" checked="true">Do not include</option>
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65 </param>
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66 <when value="use_anno">
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67 <param name="anno_file" type="data" format="txt" optional="true" label="Annotation file" help="text file with the first column listing each sample and remaining columns reserved for annotation" />
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68
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69
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70 </when>
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71 </conditional>
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72 <conditional name="include_gistic">
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73 <param name="gistic" type="select" display="radio" label="Optional: include GISTIC output in display">
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74 <option value="use_gistic" checked="false">Include</option>
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75 <option value="no_gistic" checked="true">Do not include</option>
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76 </param>
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77 <when value="use_gistic">
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78 <param name="file1" type="data" format="txt" label="all_lesions" help="all_lesions output from GISTIC" />
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79 <param name="file2" type="data" format="txt" label="amp_genes" help="amp_genes output from GISTIC" />
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80 <param name="file3" type="data" format="txt" label="del_genes" help="del_genes output from GISTIC" />
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81 </when>
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82 </conditional>
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83 </inputs>
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84
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85 <outputs>
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86 <data format="pdf" name="output_plot"/>
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87 </outputs>
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88 <citations>
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89 <citation type="bibtex">
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90 @article {Albuquerque089631,
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91 author = {Albuquerque, Marco A and Grande, Bruno M and Ritch, Elie and Jessa, Selin and Krzywinski, Martin I and Grewal, Jasleen and Shah, Sohrab and Boutros, Paul and Morin, Ryan},
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92 title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
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93 year = {2016},
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94 doi = {10.1101/089631},
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95 publisher = {Cold Spring Harbor Labs Journals},
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96 URL = {http://biorxiv.org/content/early/2016/11/26/089631},
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97 eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
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98 journal = {bioRxiv}
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99 }
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100
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101 </citation>
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102 <citation type="bibtex">
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103 @misc{
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104 goecks2010galaxy,
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105 title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
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106 author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
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107 journal={Genome Biol},
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108 volume={11},
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109 number={8},
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110 pages={R86},
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111 year={2010}
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112 }
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113 </citation>
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114 <citation type="doi">10.1101/052662</citation>
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115 </citations>
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116 </tool>
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