Mercurial > repos > vijay > pancancer_map_mutation_class

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:31:49 +0000
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54c85c40dce1 "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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1 <macros>
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2 <token name="@VERSION@">0.1.9</token>
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3
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">papaa</requirement>
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7 </requirements>
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8 </xml>
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9
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10 <xml name="stdio">
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11 <stdio>
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12 <exit_code level="fatal" range="1:"/>
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13 </stdio>
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14 </xml>
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15
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16 <xml name="inputs_basic">
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17 <param argument="--x_matrix" label="Filename of features to use in model" name="x_matrix" optional="true" type="data" format="tabular" help="data/pancan_rnaseq_freeze.tsv.gz"/>
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18 <yield/>
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19 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>
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20 <param argument="--filename_mut_burden" label="Filename of mutation burden" name="filename_mut_burden" optional="true" type="data" format="tabular" help="data/mutation_burden_freeze.tsv"/>
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21 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
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22 </xml>
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23
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24 <token name="@INPUTS_BASIC@"><![CDATA[
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25 #if $x_matrix and $x_matrix is not None:
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26 --x_matrix '$x_matrix'
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27 #end if
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28 #if $filename_mut and $filename_mut is not None:
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29 --filename_mut '$filename_mut'
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30 #end if
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31 #if $filename_mut_burden and $filename_mut_burden is not None:
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32 --filename_mut_burden '$filename_mut_burden'
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33 #end if
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34 #if $filename_sample and $filename_sample is not None:
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35 --filename_sample '$filename_sample'
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36 #end if
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37 ]]>
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38 </token>
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39
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40 <xml name="inputs_genes_diseases">
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41 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
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42 <param argument="--diseases" label="Comma sep string of TCGA disease acronyms. If no arguments are passed, filtering will default to options given in --filter_count and --filter_prop." name="diseases" optional="true" type="text" value="BLCA,BRCA,CESC,COAD,ESCA,LUAD,LUSC,OV,PRAD,READ,STAD,UCEC,UCS"/>
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43 </xml>
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44
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45 <token name="@INPUTS_GENES_DISEASES@"><![CDATA[
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46 #if $genes and $genes is not None:
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47 --genes '$genes'
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48 #end if
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49 #if $diseases and str($diseases) != '':
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50 --diseases '$diseases'
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51 #end if
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52 ]]>
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53 </token>
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54
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55
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56 <xml name="input_filename_raw_mut">
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57 <param argument="--filename_raw_mut" label="Filename of raw mut MAF" name="filename_raw_mut" optional="true" type="data" format="tabular" help="data/raw/mc3.v0.2.8.PUBLIC.maf"/>
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58 </xml>
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59
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60 <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[
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61 #if $filename_raw_mut and $filename_raw_mut is not None:
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62 --filename_raw_mut '$filename_raw_mut'
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63 #end if
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64 ]]>
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65 </token>
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66
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67
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68 <xml name="input_filename_burden">
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69 <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>
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70 </xml>
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71
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72 <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[
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73 #if $filename_burden and $filename_burden is not None:
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74 --filename_burden '$filename_burden'
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75 #end if
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76 ]]>
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77 </token>
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78
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79 <xml name="input_filename_snaptron_samples">
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80 <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>
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81 </xml>
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82
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83 <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[
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84 #if $sample_file and $sample_file is not None:
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85 --sample_file '$sample_file'
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86 #end if
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87 ]]>
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88 </token>
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89
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90
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91 <xml name="input_filename_snaptron_junctions">
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92 <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/>
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93 </xml>
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94
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95 <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[
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96 #if $junction_file and $junction_file is not None:
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97 --junction_file '$junction_file'
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98 #end if
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99 ]]>
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100 </token>
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101
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102 <xml name="inputs_copy_number_file">
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103 <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="true" type="data" format="tabular" help="data/copy_number_loss_status.tsv.gz"/>
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104 <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="true" type="data" format="tabular" help="data/copy_number_gain_status.tsv.gz"/>
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105 </xml>
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106
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107 <xml name="inputs_copy_number_class_file">
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108 <expand macro="inputs_copy_number_file" />
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109 <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="true" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>
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110 </xml>
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111
54c85c40dce1 "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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112 <xml name="inputs_copy_number_file_conditional">
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113 <conditional name="copy_number_conditional">
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114 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
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115 <when value="--copy_number">
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116 <expand macro="inputs_copy_number_file" />
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117 </when>
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118 <when value=""/>
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119 </conditional>
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120 </xml>
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121
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122 <xml name="inputs_copy_number_class_file_conditional">
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123 <conditional name="copy_number_conditional">
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124 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
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125 <when value="--copy_number">
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126 <expand macro="inputs_copy_number_class_file" />
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127 </when>
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128 <when value=""/>
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129 </conditional>
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130 </xml>
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131
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132 <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[
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133 #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})()
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134 ]]>
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135 </token>
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136
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137 <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[
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138 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
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139 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
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140 #end if
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141 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
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142 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
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143 #end if
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144 ]]>
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145 </token>
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146
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147 <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[
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148 #if $copy_number_conditional.copy_number
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149 $copy_number_conditional.copy_number
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150 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
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151 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
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152 #end if
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153 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
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154 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
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155 #end if
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156 ##@INPUTS_COPY_NUMBER_FILE@
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157 #end if
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158 ]]>
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159 </token>
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160
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161 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[
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162 #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain,'filename_cancer_gene_classification':$filename_cancer_gene_classification})()
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163 ]]>
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164 </token>
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165
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166 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[
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167 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
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168 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
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169 #end if
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170 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
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171 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
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172 #end if
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173 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
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174 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
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175 #end if
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176 ]]>
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177 </token>
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178
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179 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[
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180 #if $copy_number_conditional.copy_number
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181 $copy_number_conditional.copy_number
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182 ##
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183 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
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184 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
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185 #end if
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186 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
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187 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
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188 #end if
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189 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
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190 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
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191 #end if
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192 ##@INPUTS_COPY_NUMBER_CLASS_FILE@
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193 #end if
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194 ]]>
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195 </token>
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196
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197 <xml name="input_remove_hyper">
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198 <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>
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199 </xml>
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200 <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>
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201
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202 <xml name="input_alphas">
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203 <param argument="--alphas" label="the alphas for parameter sweep" name="alphas" optional="true" type="text" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/>
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204 </xml>
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205
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206 <token name="@INPUTS_ALPHAS@"><![CDATA[
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207 #if $alphas and $alphas is not None:
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208 --alphas '$alphas'
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209 #end if
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210 ]]>
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211 </token>
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212
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213 <xml name="input_l1_ratios">
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214 <param argument="--l1_ratios" label="the l1 ratios for parameter sweep" name="l1_ratios" optional="true" type="text" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/>
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215 </xml>
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216
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217 <token name="@INPUTS_L1_RATIOS@"><![CDATA[
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218 #if $l1_ratios and $l1_ratios is not None:
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219 --l1_ratios '$l1_ratios'
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220 #end if
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221 ]]>
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222 </token>
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223 <xml name="citations">
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224 <citations>
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225 <yield />
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226 </citations>
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227 </xml>
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228 </macros>
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229