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1 <tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
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2 <requirements>
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3 <requirement type="package" version="2.2.1">requests</requirement>
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4 <requirement type="python-module">requests</requirement>
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5 </requirements>
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6 <description>CHASM score using CRAVAT webservice</description>
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7 <command interpreter="python">
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8 chasm_webservice.py --path $input
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9 --analysis_type $analysis_type
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10 --cancertype $tissue_type
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11 --email $__user_email__
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12 --gene_analysis_out $gene_analysis_out
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13 --variant_analysis_out $variant_analysis_out
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14 --amino_acid_level_analysis_out $amino_acid_level_analysis_out
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15 --error_file $error_file
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16 </command>
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17 <inputs>
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18 <param format="txt" name="input" type="data" label="Variants File" />
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19 <param name="analysis_type" type="select" label="Choose analysis type" help="
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20 Cancer driver analysis predicts whether\
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21 the submitted variants are cancer drivers.\
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22 Functional effect analysis predicts whether\
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23 the submitted variants will have any\
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24 functional effect on their translated proteins.\
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25 Annotation only provides\
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26 GeneCard and PubMed information on\
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27 the genes containing the submitted variants.">
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28 <option value="driver">Cancer driver analysis</option>
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29 <option value="functional">Functional effect analysis</option>
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30 <option value="geneannotationonly">Annotation only</option>
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31 </param>
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32
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33 <param name="gene_annotation" type="select" label="Include Gene annotation">
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34 <option value="no">No</option>
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35 <option value="yes">Yes</option>
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36 </param>
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37
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38 <param name="tissue_type" type="select" label="Tissue Type">
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39 <option value="Bladder">Bladder</option>
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40 <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
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41 <option value="Blood-Myeloid">Blood-Myeloid</option>
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42 <option value="Brain-Cerebellum">Brain-Cerebellum</option>
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43 <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option>
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44 <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option>
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45 <option value="Breast">Breast</option>
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46 <option value="Cervix">Cervix</option>
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47 <option value="Colon">Colon</option>
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48 <option value="Head_and_Neck">Head_and_Neck</option>
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49 <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
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50 <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option>
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51 <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option>
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52 <option value="Liver-Nonviral">Liver-Nonviral</option>
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53 <option value="Liver-Viral">Liver-Viral</option>
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54 <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
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55 <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option>
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56 <option value="Melanoma">Melanoma</option>
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57 <option value="Other">Other</option>
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58 <option value="Ovary">Ovary</option>
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59 <option value="Pancreas">Pancreas</option>
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60 <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
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61 <option value="Rectum">Rectum</option>
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62 <option value="Skin">Skin</option>
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63 <option value="Stomach">Stomach</option>
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64 <option value="Thyroid">Thyroid</option>
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65 <option value="Uterus">Uterus</option>
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66 </param>
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67 </inputs>
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68 <outputs>
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69 <data format="tabular" name="gene_analysis_out" label="${tool.name} on ${on_string}: genes" />
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70 <data format="tabular" name="variant_analysis_out" label="${tool.name} on ${on_string}: variant" />
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71 <data format="tabular" name="amino_acid_level_analysis_out" label="${tool.name} on ${on_string}: aminoacid" />
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72 <data format="tabular" name="error_file" label="${tool.name} on ${on_string}: error" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input" value="chasm_input.txt"/>
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77 <param name="gene_annotation" value="yes"/>
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78 <param name="analysis_type" value="driver"/>
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79 <param name="tissue_type" value="Other"/>
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80 <output name="gene_analysis_out" file="chasm_output_genes.txt"/>
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81 <output name="variant_analysis_out" file="chasm_output_variants.txt"/>
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82 <output name="amino_acid_level_analysis_out" file="chasm_output_aminoacids.txt"/>
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83 <output name="error_file" file="chasm_output_error.txt"/>
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84 </test>
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85 </tests>
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86
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87 <help>
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88 **What it does**
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89
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90
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91 CRAVAT: Cancer-Related Analysis of VAriants Toolkit is a web server with simple interface where cancer-related analysis of variants are performed. To cite CRAVAT, please use this article.
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92
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93 CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST
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94
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95 **Input**
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96
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97 -Comment lines start with ">", "#", or "!".
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98
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99
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100 -Data fields are separated by a tab or a space.
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101
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102
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103 -The following two formats can be used for input data, but all the data rows should be in the same format:
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104
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105 .. class:: infomark
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106
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107 Genomic-coordinate format (separated by a tab or a space):
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108
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109
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110 # UID / Chr. / Position / Strand / Ref. base / Alt. base / Sample ID (optional)
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111 TR1 chr17 7577506 - G T TCGA-02-0231
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112
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113
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114 TR2 chr10 123279680 - G A TCGA-02-3512
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115
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116
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117 TR3 chr13 49033967 + C A TCGA-02-3532
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118
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119
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120 TR4 chr7 116417505 + G T TCGA-02-1523
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121
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122
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123 TR5 chr7 140453136 - T A TCGA-02-0023
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124
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125
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126 TR6 chr17 37880998 + G T TCGA-02-0252
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127
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128
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129 Ins1 chr17 37880998 + G GT TCGA-02-0252
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130
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131
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132 Del1 chr17 37880998 + GA G TCGA-02-0252
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133
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134
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135 CSub1 chr2 39871235 + ATGCT GA TCGA-02-0252
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136
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137
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138
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139 Position is a 1-based open coordinate. For insertions and deletions, use the base before the insertion or the
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140 first base of the deletion as the reference base. If you do not have strand information from your sequencing results,
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141 it is likely that they are all reported on the + strand.
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142 Make sure that your reported reference base matches the base in the reported position in the
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143 hg19 reference sequence (or hg18 if you checked hg18 checkbox).
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144
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145 .. class:: infomark
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146
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147 Amino-acid residue substitution format (separated by a tab or a space):
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148
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149
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150 # UID / Transcript / AA change / Sample ID (optional)
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151
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152
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153 TR1 NM_001126116.1 D127Y TCGA-02-0231
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154
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155
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156 TR2 NM_001144919.1 R162Q TCGA-02-3512
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157
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158
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159 TR3 NM_000321.2 Q702K TCGA-02-3532
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160
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161
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162 TR4 NM_000245.2 A1108S TCGA-02-1523
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163
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164
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165 TR5 NM_004333.4 V600E TCGA-02-0023
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166
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167
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168 TR6 NM_001005862.1 G746V TCGA-02-0252
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169
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170
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171 trascript identifier can be from either NCBI Refseq, CCDS, or Ensembl.
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172 Refseq and CCDS accessions can be specified without version numbers.
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173 The format of "AA change" column is (reference AA)(AA position)(alternate AA), without "(" and ")".
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174 Reference and alternate AAs should be from the 20 essential amino acids and each of them should be one amino acid-long.
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175
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176
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177 **Analysis**
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178
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179
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180 .. class:: infomark
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181
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182
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183 Analysis Type:
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184
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185
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186 -*Cancer driver analysis*: This analysis predicts whether the submitted variants are cancer drivers or not.
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187
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188
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189 -*Functional effect analysis*: This analysis predicts whether the submitted variants will have any functional effect on their translated proteins or not.
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190
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191
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192 -*Gene annotation only*: This analysis provides GeneCard and PubMed information on the genes containing the submitted variants.
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193
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194
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195 Currently, the following tissue types can be chosen at CRAVAT.
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196
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197
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198 Name Full name Source Date
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199
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200
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201 Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013
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202
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203
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204 Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013
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205
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206
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207 Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013
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208
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209
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210 Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010
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211
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212
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213 Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013
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214
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215
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216 Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013
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217
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218
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219 Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012
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220
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221
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222 Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013
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223
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224
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225 Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013
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226
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227
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228 Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013
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229
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230
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231 Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013
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232
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233
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234 Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013
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235
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236
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237 Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013
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238
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239
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240 Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013
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241
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242
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243 Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013
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244
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245
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246 Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013
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247
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248
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249 Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013
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250
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251
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252 Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011
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253
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254
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255 Other General purpose OV (TCGA) Jun 2013
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256
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257
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258 Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013
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259
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260
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261 Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013
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262
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263
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264 Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013
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265
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266
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267 Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013
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268
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269
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270 Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013
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271
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272
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273 Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013
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274
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275
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276 Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013
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277
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278
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279 Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013
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280
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281 **Citation**
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282
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283 If you use this tool please cite:
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284
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285 Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013). CRAVAT: Cancer-Related Analysis of VAriants Toolkit Bioinformatics, 29(5):647-648.
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286
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287 </help>
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288 </tool>
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