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2
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1 <tool id="ngs.plot" name="ngs.plot">
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2
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3 <requirements>
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4 <requirement type="package" version="2.47.1">ngsplot</requirement>
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5 </requirements>
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6
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7 <command interpreter="perl">
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8 #if $numsamples.numsamples2 == "1":
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9 runNGSplot.pl
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10 $genome_name
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11 $genomic_region_source_type.genomic_region
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12 $genomic_region_source_type.further_information
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13 $genomic_region_source_type.interval_size
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14 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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15 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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16 $numsamples.numsamples2
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17 $numsamples.usepair.usepair1
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18
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19 $numsamples.usepair.bamfile1
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20 $numsamples.usepair.reffile1
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21 $numsamples.usepair.genelist1.usegenelist1
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22 $numsamples.usepair.genelist1.genelist1
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23 $numsamples.usepair.title1
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24 $numsamples.usepair.fraglen1
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25 $numsamples.usepair.linecol1
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26
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27 $gene_database
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28 $randomly_sample
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29 $GO.gene_order
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30 $GO.KNC
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31 $GO.MIT
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32 $GO.NRS
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33 $chunk_size
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34 $quality_requirement
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35 $standard_error
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36 $radius_size
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37 $flooding_fraction
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38 $smooth_method
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39 $shaded_area
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40 $out_zip $out_avg_png $out_hm_png
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41
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42 #else if $numsamples.numsamples2 == "2":
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43 runNGSplot.pl
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44 $genome_name
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45 $genomic_region_source_type.genomic_region
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46 $genomic_region_source_type.further_information
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47 $genomic_region_source_type.interval_size
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48 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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49 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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50 $numsamples.numsamples2
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51 $numsamples.usepair.usepair1
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52
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53 $numsamples.usepair.bamfile1
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54 $numsamples.usepair.reffile1
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55 $numsamples.usepair.genelist1.usegenelist1
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56 $numsamples.usepair.genelist1.genelist1
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57 $numsamples.usepair.title1
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58 $numsamples.usepair.fraglen1
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59 $numsamples.usepair.linecol1
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60
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61 $numsamples.usepair.bamfile2
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62 $numsamples.usepair.reffile2
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63 $numsamples.usepair.genelist2.usegenelist2
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64 $numsamples.usepair.genelist2.genelist2
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65 $numsamples.usepair.title2
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66 $numsamples.usepair.fraglen2
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67 $numsamples.usepair.linecol2
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68
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69 $gene_database
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70 $randomly_sample
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71 $GO.gene_order
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72 $GO.KNC
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73 $GO.MIT
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74 $GO.NRS
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75 $chunk_size
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76 $quality_requirement
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77 $standard_error
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78 $radius_size
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79 $flooding_fraction
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80 $smooth_method
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81 $shaded_area
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82 $out_zip $out_avg_png $out_hm_png
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83
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84 #else if $numsamples.numsamples2 == "3":
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85 runNGSplot.pl
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86 $genome_name
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87 $genomic_region_source_type.genomic_region
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88 $genomic_region_source_type.further_information
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89 $genomic_region_source_type.interval_size
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90 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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91 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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92 $numsamples.numsamples2
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93 $numsamples.usepair.usepair1
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94
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95 $numsamples.usepair.bamfile1
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96 $numsamples.usepair.reffile1
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97 $numsamples.usepair.genelist1.usegenelist1
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98 $numsamples.usepair.genelist1.genelist1
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99 $numsamples.usepair.title1
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100 $numsamples.usepair.fraglen1
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101 $numsamples.usepair.linecol1
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102
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103 $numsamples.usepair.bamfile2
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104 $numsamples.usepair.reffile2
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105 $numsamples.usepair.genelist2.usegenelist2
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106 $numsamples.usepair.genelist2.genelist2
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107 $numsamples.usepair.title2
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108 $numsamples.usepair.fraglen2
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109 $numsamples.usepair.linecol2
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110
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111 $numsamples.usepair.bamfile3
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112 $numsamples.usepair.reffile3
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113 $numsamples.usepair.genelist3.usegenelist3
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114 $numsamples.usepair.genelist3.genelist3
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115 $numsamples.usepair.title3
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116 $numsamples.usepair.fraglen3
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117 $numsamples.usepair.linecol3
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118
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119 $gene_database
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120 $randomly_sample
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121 $GO.gene_order
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122 $GO.KNC
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123 $GO.MIT
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124 $GO.NRS
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125 $chunk_size
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126 $quality_requirement
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127 $standard_error
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128 $radius_size
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129 $flooding_fraction
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130 $smooth_method
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131 $shaded_area
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132 $out_zip $out_avg_png $out_hm_png
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133
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134 #else if $numsamples.numsamples2 == "4":
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135 runNGSplot.pl
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136 $genome_name
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137 $genomic_region_source_type.genomic_region
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138 $genomic_region_source_type.further_information
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139 $genomic_region_source_type.interval_size
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140 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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141 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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142 $numsamples.numsamples2
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143 $numsamples.usepair.usepair1
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144
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145 $numsamples.usepair.bamfile1
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146 $numsamples.usepair.reffile1
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147 $numsamples.usepair.genelist1.usegenelist1
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148 $numsamples.usepair.genelist1.genelist1
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149 $numsamples.usepair.title1
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150 $numsamples.usepair.fraglen1
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151 $numsamples.usepair.linecol1
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152
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153 $numsamples.usepair.bamfile2
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154 $numsamples.usepair.reffile2
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155 $numsamples.usepair.genelist2.usegenelist2
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156 $numsamples.usepair.genelist2.genelist2
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157 $numsamples.usepair.title2
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158 $numsamples.usepair.fraglen2
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159 $numsamples.usepair.linecol2
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160
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161 $numsamples.usepair.bamfile3
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162 $numsamples.usepair.reffile3
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163 $numsamples.usepair.genelist3.usegenelist3
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164 $numsamples.usepair.genelist3.genelist3
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165 $numsamples.usepair.title3
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166 $numsamples.usepair.fraglen3
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167 $numsamples.usepair.linecol3
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168
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169 $numsamples.usepair.bamfile4
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170 $numsamples.usepair.reffile4
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171 $numsamples.usepair.genelist4.usegenelist4
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172 $numsamples.usepair.genelist4.genelist4
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173 $numsamples.usepair.title4
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174 $numsamples.usepair.fraglen4
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175 $numsamples.usepair.linecol4
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176
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177 $gene_database
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178 $randomly_sample
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179 $GO.gene_order
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180 $GO.KNC
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181 $GO.MIT
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182 $GO.NRS
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183 $chunk_size
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184 $quality_requirement
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185 $standard_error
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186 $radius_size
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187 $flooding_fraction
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188 $smooth_method
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189 $shaded_area
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190 $out_zip $out_avg_png $out_hm_png
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191
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192 #else if $numsamples.numsamples2 == "5":
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193 runNGSplot.pl
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194 $genome_name
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195 $genomic_region_source_type.genomic_region
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196 $genomic_region_source_type.further_information
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197 $genomic_region_source_type.interval_size
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198 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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199 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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200 $numsamples.numsamples2
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201 $numsamples.usepair.usepair1
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202
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203 $numsamples.usepair.bamfile1
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204 $numsamples.usepair.reffile1
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205 $numsamples.usepair.genelist1.usegenelist1
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206 $numsamples.usepair.genelist1.genelist1
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207 $numsamples.usepair.title1
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208 $numsamples.usepair.fraglen1
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209 $numsamples.usepair.linecol1
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210
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211 $numsamples.usepair.bamfile2
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212 $numsamples.usepair.reffile2
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213 $numsamples.usepair.genelist2.usegenelist2
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214 $numsamples.usepair.genelist2.genelist2
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215 $numsamples.usepair.title2
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216 $numsamples.usepair.fraglen2
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217 $numsamples.usepair.linecol2
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218
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219 $numsamples.usepair.bamfile3
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220 $numsamples.usepair.reffile3
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221 $numsamples.usepair.genelist3.usegenelist3
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222 $numsamples.usepair.genelist3.genelist3
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223 $numsamples.usepair.title3
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224 $numsamples.usepair.fraglen3
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225 $numsamples.usepair.linecol3
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226
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227 $numsamples.usepair.bamfile4
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228 $numsamples.usepair.reffile4
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229 $numsamples.usepair.genelist4.usegenelist4
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230 $numsamples.usepair.genelist4.genelist4
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231 $numsamples.usepair.title4
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232 $numsamples.usepair.fraglen4
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233 $numsamples.usepair.linecol4
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234
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235 $numsamples.usepair.bamfile5
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236 $numsamples.usepair.reffile5
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237 $numsamples.usepair.genelist5.usegenelist5
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238 $numsamples.usepair.genelist5.genelist5
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239 $numsamples.usepair.title5
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240 $numsamples.usepair.fraglen5
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241 $numsamples.usepair.linecol5
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242
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243 $gene_database
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244 $randomly_sample
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245 $GO.gene_order
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246 $GO.KNC
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247 $GO.MIT
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248 $GO.NRS
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249 $chunk_size
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250 $quality_requirement
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251 $standard_error
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252 $radius_size
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253 $flooding_fraction
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254 $smooth_method
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255 $shaded_area
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256 $out_zip $out_avg_png $out_hm_png
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257
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258 #else if $numsamples.numsamples2 == "6":
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259 runNGSplot.pl
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260 $genome_name
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261 $genomic_region_source_type.genomic_region
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262 $genomic_region_source_type.further_information
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263 $genomic_region_source_type.interval_size
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264 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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265 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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266 $numsamples.numsamples2
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267 $numsamples.usepair.usepair1
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268
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269 $numsamples.usepair.bamfile1
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270 $numsamples.usepair.reffile1
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271 $numsamples.usepair.genelist1.usegenelist1
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272 $numsamples.usepair.genelist1.genelist1
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273 $numsamples.usepair.title1
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274 $numsamples.usepair.fraglen1
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275 $numsamples.usepair.linecol1
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276
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277 $numsamples.usepair.bamfile2
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278 $numsamples.usepair.reffile2
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279 $numsamples.usepair.genelist2.usegenelist2
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280 $numsamples.usepair.genelist2.genelist2
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281 $numsamples.usepair.title2
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282 $numsamples.usepair.fraglen2
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283 $numsamples.usepair.linecol2
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284
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285 $numsamples.usepair.bamfile3
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286 $numsamples.usepair.reffile3
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287 $numsamples.usepair.genelist3.usegenelist3
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288 $numsamples.usepair.genelist3.genelist3
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289 $numsamples.usepair.title3
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290 $numsamples.usepair.fraglen3
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291 $numsamples.usepair.linecol3
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292
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293 $numsamples.usepair.bamfile4
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294 $numsamples.usepair.reffile4
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295 $numsamples.usepair.genelist4.usegenelist4
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296 $numsamples.usepair.genelist4.genelist4
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297 $numsamples.usepair.title4
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298 $numsamples.usepair.fraglen4
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299 $numsamples.usepair.linecol4
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300
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301 $numsamples.usepair.bamfile5
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302 $numsamples.usepair.reffile5
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303 $numsamples.usepair.genelist5.usegenelist5
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304 $numsamples.usepair.genelist5.genelist5
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305 $numsamples.usepair.title5
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306 $numsamples.usepair.fraglen5
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307 $numsamples.usepair.linecol5
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308
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309 $numsamples.usepair.bamfile6
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310 $numsamples.usepair.reffile6
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311 $numsamples.usepair.genelist6.usegenelist6
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312 $numsamples.usepair.genelist6.genelist6
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313 $numsamples.usepair.title6
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314 $numsamples.usepair.fraglen6
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315 $numsamples.usepair.linecol6
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316
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317 $gene_database
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318 $randomly_sample
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319 $GO.gene_order
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320 $GO.KNC
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321 $GO.MIT
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322 $GO.NRS
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323 $chunk_size
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324 $quality_requirement
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325 $standard_error
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326 $radius_size
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327 $flooding_fraction
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328 $smooth_method
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329 $shaded_area
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330 $out_zip $out_avg_png $out_hm_png
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331
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332 #else if $numsamples.numsamples2 == "7":
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333 runNGSplot.pl
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334 $genome_name
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335 $genomic_region_source_type.genomic_region
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336 $genomic_region_source_type.further_information
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337 $genomic_region_source_type.interval_size
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338 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
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339 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
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340 $numsamples.numsamples2
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341 $numsamples.usepair.usepair1
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342
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343 $numsamples.usepair.bamfile1
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344 $numsamples.usepair.reffile1
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345 $numsamples.usepair.genelist1.usegenelist1
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346 $numsamples.usepair.genelist1.genelist1
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347 $numsamples.usepair.title1
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348 $numsamples.usepair.fraglen1
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349 $numsamples.usepair.linecol1
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350
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351 $numsamples.usepair.bamfile2
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352 $numsamples.usepair.reffile2
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353 $numsamples.usepair.genelist2.usegenelist2
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354 $numsamples.usepair.genelist2.genelist2
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355 $numsamples.usepair.title2
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356 $numsamples.usepair.fraglen2
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357 $numsamples.usepair.linecol2
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358
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359 $numsamples.usepair.bamfile3
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360 $numsamples.usepair.reffile3
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361 $numsamples.usepair.genelist3.usegenelist3
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362 $numsamples.usepair.genelist3.genelist3
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363 $numsamples.usepair.title3
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364 $numsamples.usepair.fraglen3
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365 $numsamples.usepair.linecol3
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366
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367 $numsamples.usepair.bamfile4
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368 $numsamples.usepair.reffile4
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369 $numsamples.usepair.genelist4.usegenelist4
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370 $numsamples.usepair.genelist4.genelist4
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371 $numsamples.usepair.title4
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372 $numsamples.usepair.fraglen4
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373 $numsamples.usepair.linecol4
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374
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375 $numsamples.usepair.bamfile5
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376 $numsamples.usepair.reffile5
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377 $numsamples.usepair.genelist5.usegenelist5
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378 $numsamples.usepair.genelist5.genelist5
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379 $numsamples.usepair.title5
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380 $numsamples.usepair.fraglen5
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381 $numsamples.usepair.linecol5
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382
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383 $numsamples.usepair.bamfile6
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384 $numsamples.usepair.reffile6
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385 $numsamples.usepair.genelist6.usegenelist6
|
|
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386 $numsamples.usepair.genelist6.genelist6
|
|
|
387 $numsamples.usepair.title6
|
|
|
388 $numsamples.usepair.fraglen6
|
|
|
389 $numsamples.usepair.linecol6
|
|
|
390
|
|
|
391 $numsamples.usepair.bamfile7
|
|
|
392 $numsamples.usepair.reffile7
|
|
|
393 $numsamples.usepair.genelist7.usegenelist7
|
|
|
394 $numsamples.usepair.genelist7.genelist7
|
|
|
395 $numsamples.usepair.title7
|
|
|
396 $numsamples.usepair.fraglen7
|
|
|
397 $numsamples.usepair.linecol7
|
|
|
398
|
|
|
399 $gene_database
|
|
|
400 $randomly_sample
|
|
|
401 $GO.gene_order
|
|
|
402 $GO.KNC
|
|
|
403 $GO.MIT
|
|
|
404 $GO.NRS
|
|
|
405 $chunk_size
|
|
|
406 $quality_requirement
|
|
|
407 $standard_error
|
|
|
408 $radius_size
|
|
|
409 $flooding_fraction
|
|
|
410 $smooth_method
|
|
|
411 $shaded_area
|
|
|
412 $out_zip $out_avg_png $out_hm_png
|
|
|
413
|
|
|
414 #else if $numsamples.numsamples2 == "8":
|
|
|
415 runNGSplot.pl
|
|
|
416 $genome_name
|
|
|
417 $genomic_region_source_type.genomic_region
|
|
|
418 $genomic_region_source_type.further_information
|
|
|
419 $genomic_region_source_type.interval_size
|
|
|
420 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
|
|
|
421 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
|
|
|
422 $numsamples.numsamples2
|
|
|
423 $numsamples.usepair.usepair1
|
|
|
424
|
|
|
425 $numsamples.usepair.bamfile1
|
|
|
426 $numsamples.usepair.reffile1
|
|
|
427 $numsamples.usepair.genelist1.usegenelist1
|
|
|
428 $numsamples.usepair.genelist1.genelist1
|
|
|
429 $numsamples.usepair.title1
|
|
|
430 $numsamples.usepair.fraglen1
|
|
|
431 $numsamples.usepair.linecol1
|
|
|
432
|
|
|
433 $numsamples.usepair.bamfile2
|
|
|
434 $numsamples.usepair.reffile2
|
|
|
435 $numsamples.usepair.genelist2.usegenelist2
|
|
|
436 $numsamples.usepair.genelist2.genelist2
|
|
|
437 $numsamples.usepair.title2
|
|
|
438 $numsamples.usepair.fraglen2
|
|
|
439 $numsamples.usepair.linecol2
|
|
|
440
|
|
|
441 $numsamples.usepair.bamfile3
|
|
|
442 $numsamples.usepair.reffile3
|
|
|
443 $numsamples.usepair.genelist3.usegenelist3
|
|
|
444 $numsamples.usepair.genelist3.genelist3
|
|
|
445 $numsamples.usepair.title3
|
|
|
446 $numsamples.usepair.fraglen3
|
|
|
447 $numsamples.usepair.linecol3
|
|
|
448
|
|
|
449 $numsamples.usepair.bamfile4
|
|
|
450 $numsamples.usepair.reffile4
|
|
|
451 $numsamples.usepair.genelist4.usegenelist4
|
|
|
452 $numsamples.usepair.genelist4.genelist4
|
|
|
453 $numsamples.usepair.title4
|
|
|
454 $numsamples.usepair.fraglen4
|
|
|
455 $numsamples.usepair.linecol4
|
|
|
456
|
|
|
457 $numsamples.usepair.bamfile5
|
|
|
458 $numsamples.usepair.reffile5
|
|
|
459 $numsamples.usepair.genelist5.usegenelist5
|
|
|
460 $numsamples.usepair.genelist5.genelist5
|
|
|
461 $numsamples.usepair.title5
|
|
|
462 $numsamples.usepair.fraglen5
|
|
|
463 $numsamples.usepair.linecol5
|
|
|
464
|
|
|
465 $numsamples.usepair.bamfile6
|
|
|
466 $numsamples.usepair.reffile6
|
|
|
467 $numsamples.usepair.genelist6.usegenelist6
|
|
|
468 $numsamples.usepair.genelist6.genelist6
|
|
|
469 $numsamples.usepair.title6
|
|
|
470 $numsamples.usepair.fraglen6
|
|
|
471 $numsamples.usepair.linecol6
|
|
|
472
|
|
|
473 $numsamples.usepair.bamfile7
|
|
|
474 $numsamples.usepair.reffile7
|
|
|
475 $numsamples.usepair.genelist7.usegenelist7
|
|
|
476 $numsamples.usepair.genelist7.genelist7
|
|
|
477 $numsamples.usepair.title7
|
|
|
478 $numsamples.usepair.fraglen7
|
|
|
479 $numsamples.usepair.linecol7
|
|
|
480
|
|
|
481 $numsamples.usepair.bamfile8
|
|
|
482 $numsamples.usepair.reffile8
|
|
|
483 $numsamples.usepair.genelist8.usegenelist8
|
|
|
484 $numsamples.usepair.genelist8.genelist8
|
|
|
485 $numsamples.usepair.title8
|
|
|
486 $numsamples.usepair.fraglen8
|
|
|
487 $numsamples.usepair.linecol8
|
|
|
488
|
|
|
489 $gene_database
|
|
|
490 $randomly_sample
|
|
|
491 $GO.gene_order
|
|
|
492 $GO.KNC
|
|
|
493 $GO.MIT
|
|
|
494 $GO.NRS
|
|
|
495 $chunk_size
|
|
|
496 $quality_requirement
|
|
|
497 $standard_error
|
|
|
498 $radius_size
|
|
|
499 $flooding_fraction
|
|
|
500 $smooth_method
|
|
|
501 $shaded_area
|
|
|
502 $out_zip $out_avg_png $out_hm_png
|
|
|
503
|
|
|
504 #else if $numsamples.numsamples2 == "9":
|
|
|
505 runNGSplot.pl
|
|
|
506 $genome_name
|
|
|
507 $genomic_region_source_type.genomic_region
|
|
|
508 $genomic_region_source_type.further_information
|
|
|
509 $genomic_region_source_type.interval_size
|
|
|
510 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
|
|
|
511 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
|
|
|
512 $numsamples.numsamples2
|
|
|
513 $numsamples.usepair.usepair1
|
|
|
514
|
|
|
515 $numsamples.usepair.bamfile1
|
|
|
516 $numsamples.usepair.reffile1
|
|
|
517 $numsamples.usepair.genelist1.usegenelist1
|
|
|
518 $numsamples.usepair.genelist1.genelist1
|
|
|
519 $numsamples.usepair.title1
|
|
|
520 $numsamples.usepair.fraglen1
|
|
|
521 $numsamples.usepair.linecol1
|
|
|
522
|
|
|
523 $numsamples.usepair.bamfile2
|
|
|
524 $numsamples.usepair.reffile2
|
|
|
525 $numsamples.usepair.genelist2.usegenelist2
|
|
|
526 $numsamples.usepair.genelist2.genelist2
|
|
|
527 $numsamples.usepair.title2
|
|
|
528 $numsamples.usepair.fraglen2
|
|
|
529 $numsamples.usepair.linecol2
|
|
|
530
|
|
|
531 $numsamples.usepair.bamfile3
|
|
|
532 $numsamples.usepair.reffile3
|
|
|
533 $numsamples.usepair.genelist3.usegenelist3
|
|
|
534 $numsamples.usepair.genelist3.genelist3
|
|
|
535 $numsamples.usepair.title3
|
|
|
536 $numsamples.usepair.fraglen3
|
|
|
537 $numsamples.usepair.linecol3
|
|
|
538
|
|
|
539 $numsamples.usepair.bamfile4
|
|
|
540 $numsamples.usepair.reffile4
|
|
|
541 $numsamples.usepair.genelist4.usegenelist4
|
|
|
542 $numsamples.usepair.genelist4.genelist4
|
|
|
543 $numsamples.usepair.title4
|
|
|
544 $numsamples.usepair.fraglen4
|
|
|
545 $numsamples.usepair.linecol4
|
|
|
546
|
|
|
547 $numsamples.usepair.bamfile5
|
|
|
548 $numsamples.usepair.reffile5
|
|
|
549 $numsamples.usepair.genelist5.usegenelist5
|
|
|
550 $numsamples.usepair.genelist5.genelist5
|
|
|
551 $numsamples.usepair.title5
|
|
|
552 $numsamples.usepair.fraglen5
|
|
|
553 $numsamples.usepair.linecol5
|
|
|
554
|
|
|
555 $numsamples.usepair.bamfile6
|
|
|
556 $numsamples.usepair.reffile6
|
|
|
557 $numsamples.usepair.genelist6.usegenelist6
|
|
|
558 $numsamples.usepair.genelist6.genelist6
|
|
|
559 $numsamples.usepair.title6
|
|
|
560 $numsamples.usepair.fraglen6
|
|
|
561 $numsamples.usepair.linecol6
|
|
|
562
|
|
|
563 $numsamples.usepair.bamfile7
|
|
|
564 $numsamples.usepair.reffile7
|
|
|
565 $numsamples.usepair.genelist7.usegenelist7
|
|
|
566 $numsamples.usepair.genelist7.genelist7
|
|
|
567 $numsamples.usepair.title7
|
|
|
568 $numsamples.usepair.fraglen7
|
|
|
569 $numsamples.usepair.linecol7
|
|
|
570
|
|
|
571 $numsamples.usepair.bamfile8
|
|
|
572 $numsamples.usepair.reffile8
|
|
|
573 $numsamples.usepair.genelist8.usegenelist8
|
|
|
574 $numsamples.usepair.genelist8.genelist8
|
|
|
575 $numsamples.usepair.title8
|
|
|
576 $numsamples.usepair.fraglen8
|
|
|
577 $numsamples.usepair.linecol8
|
|
|
578
|
|
|
579 $numsamples.usepair.bamfile9
|
|
|
580 $numsamples.usepair.reffile9
|
|
|
581 $numsamples.usepair.genelist9.usegenelist9
|
|
|
582 $numsamples.usepair.genelist9.genelist9
|
|
|
583 $numsamples.usepair.title9
|
|
|
584 $numsamples.usepair.fraglen9
|
|
|
585 $numsamples.usepair.linecol9
|
|
|
586
|
|
|
587 $gene_database
|
|
|
588 $randomly_sample
|
|
|
589 $GO.gene_order
|
|
|
590 $GO.KNC
|
|
|
591 $GO.MIT
|
|
|
592 $GO.NRS
|
|
|
593 $chunk_size
|
|
|
594 $quality_requirement
|
|
|
595 $standard_error
|
|
|
596 $radius_size
|
|
|
597 $flooding_fraction
|
|
|
598 $smooth_method
|
|
|
599 $shaded_area
|
|
|
600 $out_zip $out_avg_png $out_hm_png
|
|
|
601
|
|
|
602 #else if $numsamples.numsamples2 == "10":
|
|
|
603 runNGSplot.pl
|
|
|
604 $genome_name
|
|
|
605 $genomic_region_source_type.genomic_region
|
|
|
606 $genomic_region_source_type.further_information
|
|
|
607 $genomic_region_source_type.interval_size
|
|
|
608 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
|
|
|
609 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
|
|
|
610 $numsamples.numsamples2
|
|
|
611 $numsamples.usepair.usepair1
|
|
|
612
|
|
|
613 $numsamples.usepair.bamfile1
|
|
|
614 $numsamples.usepair.reffile1
|
|
|
615 $numsamples.usepair.genelist1.usegenelist1
|
|
|
616 $numsamples.usepair.genelist1.genelist1
|
|
|
617 $numsamples.usepair.title1
|
|
|
618 $numsamples.usepair.fraglen1
|
|
|
619 $numsamples.usepair.linecol1
|
|
|
620
|
|
|
621 $numsamples.usepair.bamfile2
|
|
|
622 $numsamples.usepair.reffile2
|
|
|
623 $numsamples.usepair.genelist2.usegenelist2
|
|
|
624 $numsamples.usepair.genelist2.genelist2
|
|
|
625 $numsamples.usepair.title2
|
|
|
626 $numsamples.usepair.fraglen2
|
|
|
627 $numsamples.usepair.linecol2
|
|
|
628
|
|
|
629 $numsamples.usepair.bamfile3
|
|
|
630 $numsamples.usepair.reffile3
|
|
|
631 $numsamples.usepair.genelist3.usegenelist3
|
|
|
632 $numsamples.usepair.genelist3.genelist3
|
|
|
633 $numsamples.usepair.title3
|
|
|
634 $numsamples.usepair.fraglen3
|
|
|
635 $numsamples.usepair.linecol3
|
|
|
636
|
|
|
637 $numsamples.usepair.bamfile4
|
|
|
638 $numsamples.usepair.reffile4
|
|
|
639 $numsamples.usepair.genelist4.usegenelist4
|
|
|
640 $numsamples.usepair.genelist4.genelist4
|
|
|
641 $numsamples.usepair.title4
|
|
|
642 $numsamples.usepair.fraglen4
|
|
|
643 $numsamples.usepair.linecol4
|
|
|
644
|
|
|
645 $numsamples.usepair.bamfile5
|
|
|
646 $numsamples.usepair.reffile5
|
|
|
647 $numsamples.usepair.genelist5.usegenelist5
|
|
|
648 $numsamples.usepair.genelist5.genelist5
|
|
|
649 $numsamples.usepair.title5
|
|
|
650 $numsamples.usepair.fraglen5
|
|
|
651 $numsamples.usepair.linecol5
|
|
|
652
|
|
|
653 $numsamples.usepair.bamfile6
|
|
|
654 $numsamples.usepair.reffile6
|
|
|
655 $numsamples.usepair.genelist6.usegenelist6
|
|
|
656 $numsamples.usepair.genelist6.genelist6
|
|
|
657 $numsamples.usepair.title6
|
|
|
658 $numsamples.usepair.fraglen6
|
|
|
659 $numsamples.usepair.linecol6
|
|
|
660
|
|
|
661 $numsamples.usepair.bamfile7
|
|
|
662 $numsamples.usepair.reffile7
|
|
|
663 $numsamples.usepair.genelist7.usegenelist7
|
|
|
664 $numsamples.usepair.genelist7.genelist7
|
|
|
665 $numsamples.usepair.title7
|
|
|
666 $numsamples.usepair.fraglen7
|
|
|
667 $numsamples.usepair.linecol7
|
|
|
668
|
|
|
669 $numsamples.usepair.bamfile8
|
|
|
670 $numsamples.usepair.reffile8
|
|
|
671 $numsamples.usepair.genelist8.usegenelist8
|
|
|
672 $numsamples.usepair.genelist8.genelist8
|
|
|
673 $numsamples.usepair.title8
|
|
|
674 $numsamples.usepair.fraglen8
|
|
|
675 $numsamples.usepair.linecol8
|
|
|
676
|
|
|
677 $numsamples.usepair.bamfile9
|
|
|
678 $numsamples.usepair.reffile9
|
|
|
679 $numsamples.usepair.genelist9.usegenelist9
|
|
|
680 $numsamples.usepair.genelist9.genelist9
|
|
|
681 $numsamples.usepair.title9
|
|
|
682 $numsamples.usepair.fraglen9
|
|
|
683 $numsamples.usepair.linecol9
|
|
|
684
|
|
|
685 $numsamples.usepair.bamfile10
|
|
|
686 $numsamples.usepair.reffile10
|
|
|
687 $numsamples.usepair.genelist10.usegenelist10
|
|
|
688 $numsamples.usepair.genelist10.genelist10
|
|
|
689 $numsamples.usepair.title10
|
|
|
690 $numsamples.usepair.fraglen10
|
|
|
691 $numsamples.usepair.linecol10
|
|
|
692
|
|
|
693 $gene_database
|
|
|
694 $randomly_sample
|
|
|
695 $GO.gene_order
|
|
|
696 $GO.KNC
|
|
|
697 $GO.MIT
|
|
|
698 $GO.NRS
|
|
|
699 $chunk_size
|
|
|
700 $quality_requirement
|
|
|
701 $standard_error
|
|
|
702 $radius_size
|
|
|
703 $flooding_fraction
|
|
|
704 $smooth_method
|
|
|
705 $shaded_area
|
|
|
706 $out_zip $out_avg_png $out_hm_png
|
|
|
707
|
|
|
708 #end if:
|
|
|
709
|
|
|
710 </command>
|
|
|
711
|
|
|
712 <!-->
|
|
|
713 <-->
|
|
|
714
|
|
|
715 <inputs>
|
|
|
716 <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
|
|
|
717 </param>
|
|
|
718 <conditional name="genomic_region_source_type">
|
|
|
719 <param type="select" name="genomic_region" label="Genomic region" help="">
|
|
|
720 <option value="tss">TSS</option>
|
|
|
721 <option value="tes">TES</option>
|
|
|
722 <option value="genebody">Genebody</option>
|
|
|
723 <option value="exon">Exon</option>
|
|
|
724 <option value="cgi">CGI</option>
|
|
|
725 <option value="bed">Customized bed file</option>
|
|
|
726 </param>
|
|
|
727
|
|
|
728 <when value="tss">
|
|
|
729 <param type="select" name="further_information" label="Further information: Not required for TSS">
|
|
|
730 <option value="na">Not Required</option>
|
|
|
731 </param>
|
|
|
732 <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
|
|
|
733 <option value="na">Not Required</option>
|
|
|
734 </param>
|
|
|
735 <conditional name="flanking_region_option_source_type">
|
|
|
736 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
737 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
738 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
|
|
|
739 </param>
|
|
|
740 <when value="flanking_region_size">
|
|
|
741 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
742 </when>
|
|
|
743 <!--when value="flanking_floating_size">
|
|
|
744 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
745 </when-->
|
|
|
746 </conditional>
|
|
|
747 </when>
|
|
|
748 <when value="tes">
|
|
|
749 <param type="select" name="further_information" label="Further information: Not required for TES">
|
|
|
750 <option value="na">Not Required</option>
|
|
|
751 </param>
|
|
|
752 <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
|
|
|
753 <option value="na">Not Required</option>
|
|
|
754 </param>
|
|
|
755 <conditional name="flanking_region_option_source_type">
|
|
|
756 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
757 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
758 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
|
|
|
759 </param>
|
|
|
760 <when value="flanking_region_size">
|
|
|
761 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
762 </when>
|
|
|
763 <!--when value="flanking_floating_size">
|
|
|
764 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
765 </when-->
|
|
|
766 </conditional>
|
|
|
767 </when>
|
|
|
768 <when value="genebody">
|
|
|
769 <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot">
|
|
|
770 <option value="chipseq">ChIP-seq</option>
|
|
|
771 <option value="rnaseq">RNA-seq</option>
|
|
|
772 </param>
|
|
|
773 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
|
|
|
774 <option value="automatic">Default</option>
|
|
|
775 <option value="0">Small</option>
|
|
|
776 <option value="1">Large</option>
|
|
|
777 </param>
|
|
|
778 <conditional name="flanking_region_option_source_type">
|
|
|
779 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
780 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
781 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
|
|
|
782 </param>
|
|
|
783 <when value="flanking_region_size">
|
|
|
784 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
785 </when>
|
|
|
786 <when value="flanking_floating_size">
|
|
|
787 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
788 </when>
|
|
|
789 </conditional>
|
|
|
790 </when>
|
|
|
791 <when value="exon">
|
|
|
792 <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot">
|
|
|
793 <option value="canonical">Canonical</option>
|
|
|
794 <option value="variant">Variant</option>
|
|
|
795 <option value="promoter">Promoter</option>
|
|
|
796 <option value="polyA">polyA</option>
|
|
|
797 <option value="altAcceptor">altAcceptor</option>
|
|
|
798 <option value="altDonor">altDonor</option>
|
|
|
799 <option value="altBoth">altBoth</option>
|
|
|
800 </param>
|
|
|
801 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
|
|
|
802 <option value="automatic">Default</option>
|
|
|
803 <option value="0">Small</option>
|
|
|
804 <option value="1">Large</option>
|
|
|
805 </param>
|
|
|
806 <conditional name="flanking_region_option_source_type">
|
|
|
807 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
808 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
809 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
|
|
|
810 </param>
|
|
|
811 <when value="flanking_region_size">
|
|
|
812 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
813 </when>
|
|
|
814 <when value="flanking_floating_size">
|
|
|
815 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
816 </when>
|
|
|
817 </conditional>
|
|
|
818 </when>
|
|
|
819 <when value="cgi">
|
|
|
820 <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot">
|
|
|
821 <option value="ProximalPromoter">ProximalPromoter</option>
|
|
|
822 <option value="Genebody">GeneBody</option>
|
|
|
823 <option value="Genedesert">GeneDesert</option>
|
|
|
824 <option value="OtherIntergenic">OtherIntergenic</option>
|
|
|
825 <option value="Pericentromere">Pericentromere</option>
|
|
|
826 <option value="Subtelomere">Subtelomere</option>
|
|
|
827 <option value="Promoter1k">Promoter1k</option>
|
|
|
828 <option value="Promoter3k">Promoter3k</option>
|
|
|
829 </param>
|
|
|
830 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
|
|
|
831 <option value="automatic">Default</option>
|
|
|
832 <option value="0">Small</option>
|
|
|
833 <option value="1">Large</option>
|
|
|
834 </param>
|
|
|
835 <conditional name="flanking_region_option_source_type">
|
|
|
836 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
837 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
838 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
|
|
|
839 </param>
|
|
|
840 <when value="flanking_region_size">
|
|
|
841 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
842 </when>
|
|
|
843 <when value="flanking_floating_size">
|
|
|
844 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
845 </when>
|
|
|
846 </conditional>
|
|
|
847 </when>
|
|
|
848 <when value="bed">
|
|
|
849 <param type="select" name="further_information" label="Further information: Not required for bed input">
|
|
|
850 <option value="na">Not Required</option>
|
|
|
851 </param>
|
|
|
852 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
|
|
|
853 <option value="automatic">Default</option>
|
|
|
854 <option value="0">Small</option>
|
|
|
855 <option value="1">Large</option>
|
|
|
856 </param>
|
|
|
857 <conditional name="flanking_region_option_source_type">
|
|
|
858 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
|
|
|
859 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
|
|
|
860 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
|
|
|
861 </param>
|
|
|
862 <when value="flanking_region_size">
|
|
|
863 <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
|
|
|
864 </when>
|
|
|
865 <when value="flanking_floating_size">
|
|
|
866 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
|
|
|
867 </when>
|
|
|
868 </conditional>
|
|
|
869 </when>
|
|
|
870 </conditional>
|
|
|
871
|
|
|
872
|
|
|
873 <conditional name="numsamples">
|
|
|
874 <param type="select" name="numsamples2" label="Number of samples to plot">
|
|
|
875 <option value="1">1</option>
|
|
|
876 <option value="2">2</option>
|
|
|
877 <option value="3">3</option>
|
|
|
878 <option value="4">4</option>
|
|
|
879 <option value="5">5</option>
|
|
|
880 <option value="6">6</option>
|
|
|
881 <option value="7">7</option>
|
|
|
882 <option value="8">8</option>
|
|
|
883 <option value="9">9</option>
|
|
|
884 <option value="10">10</option>
|
|
|
885 </param>
|
|
|
886
|
|
|
887 <when value="1">
|
|
|
888 <conditional name="usepair">
|
|
|
889 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
890 <option value="no">No</option>
|
|
|
891 <option value="yes">Yes</option>
|
|
|
892 </param>
|
|
|
893 <when value="no">
|
|
|
894 <!-- START: 1 sample, no refpairs, entry 1-->
|
|
|
895 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
896 <param type="hidden" name="reffile1" value="na"/>
|
|
|
897 <conditional name="genelist1">
|
|
|
898 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
899 <option value="no">Plot whole genome</option>
|
|
|
900 <option value="yes">Provide restricted gene list</option>
|
|
|
901 </param>
|
|
|
902 <when value="no">
|
|
|
903 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
904 </when>
|
|
|
905 <when value="yes">
|
|
|
906 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
907 </when>
|
|
|
908 </conditional>
|
|
|
909 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
910 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
911 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
912 <!-- END: 1 sample, no refpairs, entry 1-->
|
|
|
913 </when>
|
|
|
914 <when value="yes">
|
|
|
915 <!-- START: 1 sample, yes refpairs, entry 1-->
|
|
|
916 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
917 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
918 <conditional name="genelist1">
|
|
|
919 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
920 <option value="no">Plot whole genome</option>
|
|
|
921 <option value="yes">Provide restricted gene list</option>
|
|
|
922 </param>
|
|
|
923 <when value="no">
|
|
|
924 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
925 </when>
|
|
|
926 <when value="yes">
|
|
|
927 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
928 </when>
|
|
|
929 </conditional>
|
|
|
930 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
931 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
932 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
933 <!-- END: 1 sample, yes refpairs, entry 1-->
|
|
|
934 </when>
|
|
|
935 </conditional>
|
|
|
936 </when>
|
|
|
937 <when value="2">
|
|
|
938 <conditional name="usepair">
|
|
|
939 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
940 <option value="no">No</option>
|
|
|
941 <option value="yes">Yes</option>
|
|
|
942 </param>
|
|
|
943 <when value="no">
|
|
|
944 <!-- START: 2 samples, no refpairs, entry 1-->
|
|
|
945 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
946 <param type="hidden" name="reffile1" value="na"/>
|
|
|
947 <conditional name="genelist1">
|
|
|
948 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
949 <option value="no">Plot whole genome</option>
|
|
|
950 <option value="yes">Provide restricted gene list</option>
|
|
|
951 </param>
|
|
|
952 <when value="no">
|
|
|
953 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
954 </when>
|
|
|
955 <when value="yes">
|
|
|
956 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
957 </when>
|
|
|
958 </conditional>
|
|
|
959 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
960 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
961 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
962 <!-- END: 2 samples, no refpairs, entry 1-->
|
|
|
963 <!-- START: 2 samples, no refpairs, entry 2-->
|
|
|
964 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
965 <param type="hidden" name="reffile2" value="na"/>
|
|
|
966 <conditional name="genelist2">
|
|
|
967 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
968 <option value="no">Plot whole genome</option>
|
|
|
969 <option value="yes">Provide restricted gene list</option>
|
|
|
970 </param>
|
|
|
971 <when value="no">
|
|
|
972 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
973 </when>
|
|
|
974 <when value="yes">
|
|
|
975 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
976 </when>
|
|
|
977 </conditional>
|
|
|
978 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
979 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
980 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
981 <!-- END: 2 samples, no refpairs, entry 2-->
|
|
|
982 </when>
|
|
|
983 <when value="yes">
|
|
|
984 <!-- START: 2 samples, yes refpairs, entry 1-->
|
|
|
985 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
986 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
987 <conditional name="genelist1">
|
|
|
988 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
989 <option value="no">Plot whole genome</option>
|
|
|
990 <option value="yes">Provide restricted gene list</option>
|
|
|
991 </param>
|
|
|
992 <when value="no">
|
|
|
993 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
994 </when>
|
|
|
995 <when value="yes">
|
|
|
996 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
997 </when>
|
|
|
998 </conditional>
|
|
|
999 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1000 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1001 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1002 <!-- END: 2 samples, yes refpairs, entry 1-->
|
|
|
1003 <!-- START: 2 samples, yes refpairs, entry 2-->
|
|
|
1004 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1005 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1006 <conditional name="genelist2">
|
|
|
1007 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1008 <option value="no">Plot whole genome</option>
|
|
|
1009 <option value="yes">Provide restricted gene list</option>
|
|
|
1010 </param>
|
|
|
1011 <when value="no">
|
|
|
1012 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1013 </when>
|
|
|
1014 <when value="yes">
|
|
|
1015 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1016 </when>
|
|
|
1017 </conditional>
|
|
|
1018 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1019 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1020 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1021 <!-- END: 2 samples, yes refpairs, entry 2-->
|
|
|
1022 </when>
|
|
|
1023 </conditional>
|
|
|
1024 </when>
|
|
|
1025 <when value="3">
|
|
|
1026 <conditional name="usepair">
|
|
|
1027 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
1028 <option value="no">No</option>
|
|
|
1029 <option value="yes">Yes</option>
|
|
|
1030 </param>
|
|
|
1031 <when value="no">
|
|
|
1032 <!-- START: 3 samples, no refpairs, entry 1-->
|
|
|
1033 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1034 <param type="hidden" name="reffile1" value="na"/>
|
|
|
1035 <conditional name="genelist1">
|
|
|
1036 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1037 <option value="no">Plot whole genome</option>
|
|
|
1038 <option value="yes">Provide restricted gene list</option>
|
|
|
1039 </param>
|
|
|
1040 <when value="no">
|
|
|
1041 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1042 </when>
|
|
|
1043 <when value="yes">
|
|
|
1044 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1045 </when>
|
|
|
1046 </conditional>
|
|
|
1047 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1048 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1049 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1050 <!-- END: 3 samples, no refpairs, entry 1-->
|
|
|
1051 <!-- START: 3 samples, no refpairs, entry 2-->
|
|
|
1052 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1053 <param type="hidden" name="reffile2" value="na"/>
|
|
|
1054 <conditional name="genelist2">
|
|
|
1055 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1056 <option value="no">Plot whole genome</option>
|
|
|
1057 <option value="yes">Provide restricted gene list</option>
|
|
|
1058 </param>
|
|
|
1059 <when value="no">
|
|
|
1060 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1061 </when>
|
|
|
1062 <when value="yes">
|
|
|
1063 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1064 </when>
|
|
|
1065 </conditional>
|
|
|
1066 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1067 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1068 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1069 <!-- END: 3 samples, no refpairs, entry 2-->
|
|
|
1070 <!-- START: 3 samples, no refpairs, entry 3-->
|
|
|
1071 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1072 <param type="hidden" name="reffile3" value="na"/>
|
|
|
1073 <conditional name="genelist3">
|
|
|
1074 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1075 <option value="no">Plot whole genome</option>
|
|
|
1076 <option value="yes">Provide restricted gene list</option>
|
|
|
1077 </param>
|
|
|
1078 <when value="no">
|
|
|
1079 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1080 </when>
|
|
|
1081 <when value="yes">
|
|
|
1082 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1083 </when>
|
|
|
1084 </conditional>
|
|
|
1085 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1086 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1087 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1088 <!-- END: 3 samples, no refpairs, entry 3-->
|
|
|
1089 </when>
|
|
|
1090 <when value="yes">
|
|
|
1091 <!-- START: 3 samples, yes refpairs, entry 1-->
|
|
|
1092 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1093 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
1094 <conditional name="genelist1">
|
|
|
1095 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1096 <option value="no">Plot whole genome</option>
|
|
|
1097 <option value="yes">Provide restricted gene list</option>
|
|
|
1098 </param>
|
|
|
1099 <when value="no">
|
|
|
1100 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1101 </when>
|
|
|
1102 <when value="yes">
|
|
|
1103 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1104 </when>
|
|
|
1105 </conditional>
|
|
|
1106 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1107 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1108 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1109 <!-- END: 3 samples, yes refpairs, entry 1-->
|
|
|
1110 <!-- START: 3 samples, yes refpairs, entry 2-->
|
|
|
1111 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1112 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1113 <conditional name="genelist2">
|
|
|
1114 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1115 <option value="no">Plot whole genome</option>
|
|
|
1116 <option value="yes">Provide restricted gene list</option>
|
|
|
1117 </param>
|
|
|
1118 <when value="no">
|
|
|
1119 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1120 </when>
|
|
|
1121 <when value="yes">
|
|
|
1122 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1123 </when>
|
|
|
1124 </conditional>
|
|
|
1125 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1126 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1127 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1128 <!-- END: 3 samples, yes refpairs, entry 2-->
|
|
|
1129 <!-- START: 3 samples, yes refpairs, entry 3-->
|
|
|
1130 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1131 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
1132 <conditional name="genelist3">
|
|
|
1133 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1134 <option value="no">Plot whole genome</option>
|
|
|
1135 <option value="yes">Provide restricted gene list</option>
|
|
|
1136 </param>
|
|
|
1137 <when value="no">
|
|
|
1138 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1139 </when>
|
|
|
1140 <when value="yes">
|
|
|
1141 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1142 </when>
|
|
|
1143 </conditional>
|
|
|
1144 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1145 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1146 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1147 <!-- END: 3 samples, yes refpairs, entry 2-->
|
|
|
1148 </when>
|
|
|
1149 </conditional>
|
|
|
1150 </when>
|
|
|
1151 <when value="4">
|
|
|
1152 <conditional name="usepair">
|
|
|
1153 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
1154 <option value="no">No</option>
|
|
|
1155 <option value="yes">Yes</option>
|
|
|
1156 </param>
|
|
|
1157 <when value="no">
|
|
|
1158 <!-- START: 4 samples, no refpairs, entry 1-->
|
|
|
1159 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1160 <param type="hidden" name="reffile1" value="na"/>
|
|
|
1161 <conditional name="genelist1">
|
|
|
1162 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1163 <option value="no">Plot whole genome</option>
|
|
|
1164 <option value="yes">Provide restricted gene list</option>
|
|
|
1165 </param>
|
|
|
1166 <when value="no">
|
|
|
1167 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1168 </when>
|
|
|
1169 <when value="yes">
|
|
|
1170 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1171 </when>
|
|
|
1172 </conditional>
|
|
|
1173 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1174 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1175 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1176 <!-- END: 4 samples, no refpairs, entry 1-->
|
|
|
1177 <!-- START: 4 samples, no refpairs, entry 2-->
|
|
|
1178 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1179 <param type="hidden" name="reffile2" value="na"/>
|
|
|
1180 <conditional name="genelist2">
|
|
|
1181 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1182 <option value="no">Plot whole genome</option>
|
|
|
1183 <option value="yes">Provide restricted gene list</option>
|
|
|
1184 </param>
|
|
|
1185 <when value="no">
|
|
|
1186 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1187 </when>
|
|
|
1188 <when value="yes">
|
|
|
1189 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1190 </when>
|
|
|
1191 </conditional>
|
|
|
1192 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1193 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1194 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1195 <!-- END: 4 samples, no refpairs, entry 2-->
|
|
|
1196 <!-- START: 4 samples, no refpairs, entry 3-->
|
|
|
1197 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1198 <param type="hidden" name="reffile3" value="na"/>
|
|
|
1199 <conditional name="genelist3">
|
|
|
1200 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1201 <option value="no">Plot whole genome</option>
|
|
|
1202 <option value="yes">Provide restricted gene list</option>
|
|
|
1203 </param>
|
|
|
1204 <when value="no">
|
|
|
1205 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1206 </when>
|
|
|
1207 <when value="yes">
|
|
|
1208 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1209 </when>
|
|
|
1210 </conditional>
|
|
|
1211 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1212 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1213 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1214 <!-- END: 4 samples, no refpairs, entry 3-->
|
|
|
1215 <!-- START: 4 samples, no refpairs, entry 4-->
|
|
|
1216 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1217 <param type="hidden" name="reffile4" value="na"/>
|
|
|
1218 <conditional name="genelist4">
|
|
|
1219 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1220 <option value="no">Plot whole genome</option>
|
|
|
1221 <option value="yes">Provide restricted gene list</option>
|
|
|
1222 </param>
|
|
|
1223 <when value="no">
|
|
|
1224 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1225 </when>
|
|
|
1226 <when value="yes">
|
|
|
1227 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1228 </when>
|
|
|
1229 </conditional>
|
|
|
1230 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1231 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1232 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1233 <!-- END: 4 samples, no refpairs, entry 4-->
|
|
|
1234 </when>
|
|
|
1235 <when value="yes">
|
|
|
1236 <!-- START: 4 samples, yes refpairs, entry 1-->
|
|
|
1237 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1238 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
1239 <conditional name="genelist1">
|
|
|
1240 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1241 <option value="no">Plot whole genome</option>
|
|
|
1242 <option value="yes">Provide restricted gene list</option>
|
|
|
1243 </param>
|
|
|
1244 <when value="no">
|
|
|
1245 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1246 </when>
|
|
|
1247 <when value="yes">
|
|
|
1248 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1249 </when>
|
|
|
1250 </conditional>
|
|
|
1251 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1252 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1253 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1254 <!-- END: 4 samples, yes refpairs, entry 1-->
|
|
|
1255 <!-- START: 4 samples, yes refpairs, entry 2-->
|
|
|
1256 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1257 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1258 <conditional name="genelist2">
|
|
|
1259 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1260 <option value="no">Plot whole genome</option>
|
|
|
1261 <option value="yes">Provide restricted gene list</option>
|
|
|
1262 </param>
|
|
|
1263 <when value="no">
|
|
|
1264 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1265 </when>
|
|
|
1266 <when value="yes">
|
|
|
1267 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1268 </when>
|
|
|
1269 </conditional>
|
|
|
1270 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1271 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1272 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1273 <!-- END: 4 samples, yes refpairs, entry 2-->
|
|
|
1274 <!-- START: 4 samples, yes refpairs, entry 3-->
|
|
|
1275 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1276 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
1277 <conditional name="genelist3">
|
|
|
1278 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1279 <option value="no">Plot whole genome</option>
|
|
|
1280 <option value="yes">Provide restricted gene list</option>
|
|
|
1281 </param>
|
|
|
1282 <when value="no">
|
|
|
1283 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1284 </when>
|
|
|
1285 <when value="yes">
|
|
|
1286 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1287 </when>
|
|
|
1288 </conditional>
|
|
|
1289 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1290 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1291 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1292 <!-- END: 4 samples, yes refpairs, entry 3-->
|
|
|
1293 <!-- START: 4 samples, yes refpairs, entry 4-->
|
|
|
1294 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1295 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
1296 <conditional name="genelist4">
|
|
|
1297 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1298 <option value="no">Plot whole genome</option>
|
|
|
1299 <option value="yes">Provide restricted gene list</option>
|
|
|
1300 </param>
|
|
|
1301 <when value="no">
|
|
|
1302 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1303 </when>
|
|
|
1304 <when value="yes">
|
|
|
1305 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1306 </when>
|
|
|
1307 </conditional>
|
|
|
1308 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1309 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1310 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1311 <!-- END: 4 samples, yes refpairs, entry 4-->
|
|
|
1312 </when>
|
|
|
1313 </conditional>
|
|
|
1314 </when>
|
|
|
1315 <when value="5">
|
|
|
1316 <conditional name="usepair">
|
|
|
1317 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
1318 <option value="no">No</option>
|
|
|
1319 <option value="yes">Yes</option>
|
|
|
1320 </param>
|
|
|
1321 <when value="no">
|
|
|
1322 <!-- START: 5 samples, no refpairs, entry 1-->
|
|
|
1323 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1324 <param type="hidden" name="reffile1" value="na"/>
|
|
|
1325 <conditional name="genelist1">
|
|
|
1326 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1327 <option value="no">Plot whole genome</option>
|
|
|
1328 <option value="yes">Provide restricted gene list</option>
|
|
|
1329 </param>
|
|
|
1330 <when value="no">
|
|
|
1331 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1332 </when>
|
|
|
1333 <when value="yes">
|
|
|
1334 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1335 </when>
|
|
|
1336 </conditional>
|
|
|
1337 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1338 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1339 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1340 <!-- END: 5 samples, no refpairs, entry 1-->
|
|
|
1341 <!-- START: 5 samples, no refpairs, entry 2-->
|
|
|
1342 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1343 <param type="hidden" name="reffile2" value="na"/>
|
|
|
1344 <conditional name="genelist2">
|
|
|
1345 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1346 <option value="no">Plot whole genome</option>
|
|
|
1347 <option value="yes">Provide restricted gene list</option>
|
|
|
1348 </param>
|
|
|
1349 <when value="no">
|
|
|
1350 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1351 </when>
|
|
|
1352 <when value="yes">
|
|
|
1353 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1354 </when>
|
|
|
1355 </conditional>
|
|
|
1356 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1357 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1358 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1359 <!-- END: 5 samples, no refpairs, entry 2-->
|
|
|
1360 <!-- START: 5 samples, no refpairs, entry 3-->
|
|
|
1361 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1362 <param type="hidden" name="reffile3" value="na"/>
|
|
|
1363 <conditional name="genelist3">
|
|
|
1364 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1365 <option value="no">Plot whole genome</option>
|
|
|
1366 <option value="yes">Provide restricted gene list</option>
|
|
|
1367 </param>
|
|
|
1368 <when value="no">
|
|
|
1369 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1370 </when>
|
|
|
1371 <when value="yes">
|
|
|
1372 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1373 </when>
|
|
|
1374 </conditional>
|
|
|
1375 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1376 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1377 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1378 <!-- END: 5 samples, no refpairs, entry 3-->
|
|
|
1379 <!-- START: 5 samples, no refpairs, entry 4-->
|
|
|
1380 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1381 <param type="hidden" name="reffile4" value="na"/>
|
|
|
1382 <conditional name="genelist4">
|
|
|
1383 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1384 <option value="no">Plot whole genome</option>
|
|
|
1385 <option value="yes">Provide restricted gene list</option>
|
|
|
1386 </param>
|
|
|
1387 <when value="no">
|
|
|
1388 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1389 </when>
|
|
|
1390 <when value="yes">
|
|
|
1391 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1392 </when>
|
|
|
1393 </conditional>
|
|
|
1394 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1395 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1396 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1397 <!-- END: 5 samples, no refpairs, entry 4-->
|
|
|
1398 <!-- START: 5 samples, no refpairs, entry 5-->
|
|
|
1399 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1400 <param type="hidden" name="reffile5" value="na"/>
|
|
|
1401 <conditional name="genelist5">
|
|
|
1402 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1403 <option value="no">Plot whole genome</option>
|
|
|
1404 <option value="yes">Provide restricted gene list</option>
|
|
|
1405 </param>
|
|
|
1406 <when value="no">
|
|
|
1407 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1408 </when>
|
|
|
1409 <when value="yes">
|
|
|
1410 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1411 </when>
|
|
|
1412 </conditional>
|
|
|
1413 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1414 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1415 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1416 <!-- END: 5 samples, no refpairs, entry 5-->
|
|
|
1417 </when>
|
|
|
1418 <when value="yes">
|
|
|
1419 <!-- START: 5 samples, yes refpairs, entry 1-->
|
|
|
1420 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1421 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
1422 <conditional name="genelist1">
|
|
|
1423 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1424 <option value="no">Plot whole genome</option>
|
|
|
1425 <option value="yes">Provide restricted gene list</option>
|
|
|
1426 </param>
|
|
|
1427 <when value="no">
|
|
|
1428 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1429 </when>
|
|
|
1430 <when value="yes">
|
|
|
1431 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1432 </when>
|
|
|
1433 </conditional>
|
|
|
1434 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1435 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1436 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1437 <!-- END: 5 samples, yes refpairs, entry 1-->
|
|
|
1438 <!-- START: 5 samples, yes refpairs, entry 2-->
|
|
|
1439 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1440 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1441 <conditional name="genelist2">
|
|
|
1442 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1443 <option value="no">Plot whole genome</option>
|
|
|
1444 <option value="yes">Provide restricted gene list</option>
|
|
|
1445 </param>
|
|
|
1446 <when value="no">
|
|
|
1447 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1448 </when>
|
|
|
1449 <when value="yes">
|
|
|
1450 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1451 </when>
|
|
|
1452 </conditional>
|
|
|
1453 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1454 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1455 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1456 <!-- END: 5 samples, yes refpairs, entry 2-->
|
|
|
1457 <!-- START: 5 samples, yes refpairs, entry 3-->
|
|
|
1458 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1459 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
1460 <conditional name="genelist3">
|
|
|
1461 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1462 <option value="no">Plot whole genome</option>
|
|
|
1463 <option value="yes">Provide restricted gene list</option>
|
|
|
1464 </param>
|
|
|
1465 <when value="no">
|
|
|
1466 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1467 </when>
|
|
|
1468 <when value="yes">
|
|
|
1469 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1470 </when>
|
|
|
1471 </conditional>
|
|
|
1472 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1473 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1474 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1475 <!-- END: 5 samples, yes refpairs, entry 3-->
|
|
|
1476 <!-- START: 5 samples, yes refpairs, entry 4-->
|
|
|
1477 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1478 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
1479 <conditional name="genelist4">
|
|
|
1480 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1481 <option value="no">Plot whole genome</option>
|
|
|
1482 <option value="yes">Provide restricted gene list</option>
|
|
|
1483 </param>
|
|
|
1484 <when value="no">
|
|
|
1485 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1486 </when>
|
|
|
1487 <when value="yes">
|
|
|
1488 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1489 </when>
|
|
|
1490 </conditional>
|
|
|
1491 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1492 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1493 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1494 <!-- END: 5 samples, yes refpairs, entry 4-->
|
|
|
1495 <!-- START: 5 samples, yes refpairs, entry 5-->
|
|
|
1496 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1497 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
1498 <conditional name="genelist5">
|
|
|
1499 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1500 <option value="no">Plot whole genome</option>
|
|
|
1501 <option value="yes">Provide restricted gene list</option>
|
|
|
1502 </param>
|
|
|
1503 <when value="no">
|
|
|
1504 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1505 </when>
|
|
|
1506 <when value="yes">
|
|
|
1507 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1508 </when>
|
|
|
1509 </conditional>
|
|
|
1510 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1511 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1512 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1513 <!-- END: 5 samples, yes refpairs, entry 5-->
|
|
|
1514 </when>
|
|
|
1515 </conditional>
|
|
|
1516 </when>
|
|
|
1517 <when value="6">
|
|
|
1518 <conditional name="usepair">
|
|
|
1519 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
1520 <option value="no">No</option>
|
|
|
1521 <option value="yes">Yes</option>
|
|
|
1522 </param>
|
|
|
1523 <when value="no">
|
|
|
1524 <!-- START: 6 samples, no refpairs, entry 1-->
|
|
|
1525 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1526 <param type="hidden" name="reffile1" value="na"/>
|
|
|
1527 <conditional name="genelist1">
|
|
|
1528 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1529 <option value="no">Plot whole genome</option>
|
|
|
1530 <option value="yes">Provide restricted gene list</option>
|
|
|
1531 </param>
|
|
|
1532 <when value="no">
|
|
|
1533 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1534 </when>
|
|
|
1535 <when value="yes">
|
|
|
1536 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1537 </when>
|
|
|
1538 </conditional>
|
|
|
1539 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1540 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1541 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1542 <!-- END: 6 samples, no refpairs, entry 1-->
|
|
|
1543 <!-- START: 6 samples, no refpairs, entry 2-->
|
|
|
1544 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1545 <param type="hidden" name="reffile2" value="na"/>
|
|
|
1546 <conditional name="genelist2">
|
|
|
1547 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1548 <option value="no">Plot whole genome</option>
|
|
|
1549 <option value="yes">Provide restricted gene list</option>
|
|
|
1550 </param>
|
|
|
1551 <when value="no">
|
|
|
1552 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1553 </when>
|
|
|
1554 <when value="yes">
|
|
|
1555 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1556 </when>
|
|
|
1557 </conditional>
|
|
|
1558 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1559 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1560 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1561 <!-- END: 6 samples, no refpairs, entry 2-->
|
|
|
1562 <!-- START: 6 samples, no refpairs, entry 3-->
|
|
|
1563 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1564 <param type="hidden" name="reffile3" value="na"/>
|
|
|
1565 <conditional name="genelist3">
|
|
|
1566 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1567 <option value="no">Plot whole genome</option>
|
|
|
1568 <option value="yes">Provide restricted gene list</option>
|
|
|
1569 </param>
|
|
|
1570 <when value="no">
|
|
|
1571 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1572 </when>
|
|
|
1573 <when value="yes">
|
|
|
1574 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1575 </when>
|
|
|
1576 </conditional>
|
|
|
1577 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1578 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1579 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1580 <!-- END: 6 samples, no refpairs, entry 3-->
|
|
|
1581 <!-- START: 6 samples, no refpairs, entry 4-->
|
|
|
1582 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1583 <param type="hidden" name="reffile4" value="na"/>
|
|
|
1584 <conditional name="genelist4">
|
|
|
1585 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1586 <option value="no">Plot whole genome</option>
|
|
|
1587 <option value="yes">Provide restricted gene list</option>
|
|
|
1588 </param>
|
|
|
1589 <when value="no">
|
|
|
1590 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1591 </when>
|
|
|
1592 <when value="yes">
|
|
|
1593 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1594 </when>
|
|
|
1595 </conditional>
|
|
|
1596 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1597 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1598 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1599 <!-- END: 6 samples, no refpairs, entry 4-->
|
|
|
1600 <!-- START: 6 samples, no refpairs, entry 5-->
|
|
|
1601 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1602 <param type="hidden" name="reffile5" value="na"/>
|
|
|
1603 <conditional name="genelist5">
|
|
|
1604 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1605 <option value="no">Plot whole genome</option>
|
|
|
1606 <option value="yes">Provide restricted gene list</option>
|
|
|
1607 </param>
|
|
|
1608 <when value="no">
|
|
|
1609 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1610 </when>
|
|
|
1611 <when value="yes">
|
|
|
1612 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1613 </when>
|
|
|
1614 </conditional>
|
|
|
1615 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1616 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1617 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1618 <!-- END: 6 samples, no refpairs, entry 5-->
|
|
|
1619 <!-- START: 6 samples, no refpairs, entry 6-->
|
|
|
1620 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
1621 <param type="hidden" name="reffile6" value="na"/>
|
|
|
1622 <conditional name="genelist6">
|
|
|
1623 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
1624 <option value="no">Plot whole genome</option>
|
|
|
1625 <option value="yes">Provide restricted gene list</option>
|
|
|
1626 </param>
|
|
|
1627 <when value="no">
|
|
|
1628 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
1629 </when>
|
|
|
1630 <when value="yes">
|
|
|
1631 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
1632 </when>
|
|
|
1633 </conditional>
|
|
|
1634 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
1635 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
1636 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
1637 <!-- END: 6 samples, no refpairs, entry 6-->
|
|
|
1638 </when>
|
|
|
1639 <when value="yes">
|
|
|
1640 <!-- START: 6 samples, yes refpairs, entry 1-->
|
|
|
1641 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1642 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
1643 <conditional name="genelist1">
|
|
|
1644 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1645 <option value="no">Plot whole genome</option>
|
|
|
1646 <option value="yes">Provide restricted gene list</option>
|
|
|
1647 </param>
|
|
|
1648 <when value="no">
|
|
|
1649 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1650 </when>
|
|
|
1651 <when value="yes">
|
|
|
1652 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1653 </when>
|
|
|
1654 </conditional>
|
|
|
1655 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1656 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1657 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1658 <!-- END: 6 samples, yes refpairs, entry 1-->
|
|
|
1659 <!-- START: 6 samples, yes refpairs, entry 2-->
|
|
|
1660 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1661 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1662 <conditional name="genelist2">
|
|
|
1663 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1664 <option value="no">Plot whole genome</option>
|
|
|
1665 <option value="yes">Provide restricted gene list</option>
|
|
|
1666 </param>
|
|
|
1667 <when value="no">
|
|
|
1668 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1669 </when>
|
|
|
1670 <when value="yes">
|
|
|
1671 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1672 </when>
|
|
|
1673 </conditional>
|
|
|
1674 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1675 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1676 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1677 <!-- END: 6 samples, yes refpairs, entry 2-->
|
|
|
1678 <!-- START: 6 samples, yes refpairs, entry 3-->
|
|
|
1679 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1680 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
1681 <conditional name="genelist3">
|
|
|
1682 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1683 <option value="no">Plot whole genome</option>
|
|
|
1684 <option value="yes">Provide restricted gene list</option>
|
|
|
1685 </param>
|
|
|
1686 <when value="no">
|
|
|
1687 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1688 </when>
|
|
|
1689 <when value="yes">
|
|
|
1690 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1691 </when>
|
|
|
1692 </conditional>
|
|
|
1693 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1694 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1695 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1696 <!-- END: 6 samples, yes refpairs, entry 3-->
|
|
|
1697 <!-- START: 6 samples, yes refpairs, entry 4-->
|
|
|
1698 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1699 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
1700 <conditional name="genelist4">
|
|
|
1701 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1702 <option value="no">Plot whole genome</option>
|
|
|
1703 <option value="yes">Provide restricted gene list</option>
|
|
|
1704 </param>
|
|
|
1705 <when value="no">
|
|
|
1706 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1707 </when>
|
|
|
1708 <when value="yes">
|
|
|
1709 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1710 </when>
|
|
|
1711 </conditional>
|
|
|
1712 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1713 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1714 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1715 <!-- END: 6 samples, yes refpairs, entry 4-->
|
|
|
1716 <!-- START: 6 samples, yes refpairs, entry 5-->
|
|
|
1717 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1718 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
1719 <conditional name="genelist5">
|
|
|
1720 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1721 <option value="no">Plot whole genome</option>
|
|
|
1722 <option value="yes">Provide restricted gene list</option>
|
|
|
1723 </param>
|
|
|
1724 <when value="no">
|
|
|
1725 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1726 </when>
|
|
|
1727 <when value="yes">
|
|
|
1728 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1729 </when>
|
|
|
1730 </conditional>
|
|
|
1731 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1732 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1733 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1734 <!-- END: 6 samples, yes refpairs, entry 5-->
|
|
|
1735 <!-- START: 6 samples, yes refpairs, entry 6-->
|
|
|
1736 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
1737 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
|
|
|
1738 <conditional name="genelist6">
|
|
|
1739 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
1740 <option value="no">Plot whole genome</option>
|
|
|
1741 <option value="yes">Provide restricted gene list</option>
|
|
|
1742 </param>
|
|
|
1743 <when value="no">
|
|
|
1744 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
1745 </when>
|
|
|
1746 <when value="yes">
|
|
|
1747 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
1748 </when>
|
|
|
1749 </conditional>
|
|
|
1750 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
1751 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
1752 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
1753 <!-- END: 6 samples, yes refpairs, entry 6-->
|
|
|
1754 </when>
|
|
|
1755 </conditional>
|
|
|
1756 </when>
|
|
|
1757 <when value="7">
|
|
|
1758 <conditional name="usepair">
|
|
|
1759 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
1760 <option value="no">No</option>
|
|
|
1761 <option value="yes">Yes</option>
|
|
|
1762 </param>
|
|
|
1763 <when value="no">
|
|
|
1764 <!-- START: 7 samples, no refpairs, entry 1-->
|
|
|
1765 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1766 <param type="hidden" name="reffile1" value="na"/>
|
|
|
1767 <conditional name="genelist1">
|
|
|
1768 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1769 <option value="no">Plot whole genome</option>
|
|
|
1770 <option value="yes">Provide restricted gene list</option>
|
|
|
1771 </param>
|
|
|
1772 <when value="no">
|
|
|
1773 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1774 </when>
|
|
|
1775 <when value="yes">
|
|
|
1776 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1777 </when>
|
|
|
1778 </conditional>
|
|
|
1779 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1780 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1781 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1782 <!-- END: 7 samples, no refpairs, entry 1-->
|
|
|
1783 <!-- START: 7 samples, no refpairs, entry 2-->
|
|
|
1784 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1785 <param type="hidden" name="reffile2" value="na"/>
|
|
|
1786 <conditional name="genelist2">
|
|
|
1787 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1788 <option value="no">Plot whole genome</option>
|
|
|
1789 <option value="yes">Provide restricted gene list</option>
|
|
|
1790 </param>
|
|
|
1791 <when value="no">
|
|
|
1792 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1793 </when>
|
|
|
1794 <when value="yes">
|
|
|
1795 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1796 </when>
|
|
|
1797 </conditional>
|
|
|
1798 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1799 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1800 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1801 <!-- END: 7 samples, no refpairs, entry 2-->
|
|
|
1802 <!-- START: 7 samples, no refpairs, entry 3-->
|
|
|
1803 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1804 <param type="hidden" name="reffile3" value="na"/>
|
|
|
1805 <conditional name="genelist3">
|
|
|
1806 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1807 <option value="no">Plot whole genome</option>
|
|
|
1808 <option value="yes">Provide restricted gene list</option>
|
|
|
1809 </param>
|
|
|
1810 <when value="no">
|
|
|
1811 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1812 </when>
|
|
|
1813 <when value="yes">
|
|
|
1814 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1815 </when>
|
|
|
1816 </conditional>
|
|
|
1817 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1818 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1819 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1820 <!-- END: 7 samples, no refpairs, entry 3-->
|
|
|
1821 <!-- START: 7 samples, no refpairs, entry 4-->
|
|
|
1822 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1823 <param type="hidden" name="reffile4" value="na"/>
|
|
|
1824 <conditional name="genelist4">
|
|
|
1825 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1826 <option value="no">Plot whole genome</option>
|
|
|
1827 <option value="yes">Provide restricted gene list</option>
|
|
|
1828 </param>
|
|
|
1829 <when value="no">
|
|
|
1830 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1831 </when>
|
|
|
1832 <when value="yes">
|
|
|
1833 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1834 </when>
|
|
|
1835 </conditional>
|
|
|
1836 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1837 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1838 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1839 <!-- END: 7 samples, no refpairs, entry 4-->
|
|
|
1840 <!-- START: 7 samples, no refpairs, entry 5-->
|
|
|
1841 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1842 <param type="hidden" name="reffile5" value="na"/>
|
|
|
1843 <conditional name="genelist5">
|
|
|
1844 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1845 <option value="no">Plot whole genome</option>
|
|
|
1846 <option value="yes">Provide restricted gene list</option>
|
|
|
1847 </param>
|
|
|
1848 <when value="no">
|
|
|
1849 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1850 </when>
|
|
|
1851 <when value="yes">
|
|
|
1852 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1853 </when>
|
|
|
1854 </conditional>
|
|
|
1855 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1856 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1857 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1858 <!-- END: 7 samples, no refpairs, entry 5-->
|
|
|
1859 <!-- START: 7 samples, no refpairs, entry 6-->
|
|
|
1860 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
1861 <param type="hidden" name="reffile6" value="na"/>
|
|
|
1862 <conditional name="genelist6">
|
|
|
1863 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
1864 <option value="no">Plot whole genome</option>
|
|
|
1865 <option value="yes">Provide restricted gene list</option>
|
|
|
1866 </param>
|
|
|
1867 <when value="no">
|
|
|
1868 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
1869 </when>
|
|
|
1870 <when value="yes">
|
|
|
1871 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
1872 </when>
|
|
|
1873 </conditional>
|
|
|
1874 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
1875 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
1876 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
1877 <!-- END: 7 samples, no refpairs, entry 6-->
|
|
|
1878 <!-- START: 7 samples, no refpairs, entry 7-->
|
|
|
1879 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
1880 <param type="hidden" name="reffile7" value="na"/>
|
|
|
1881 <conditional name="genelist7">
|
|
|
1882 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
1883 <option value="no">Plot whole genome</option>
|
|
|
1884 <option value="yes">Provide restricted gene list</option>
|
|
|
1885 </param>
|
|
|
1886 <when value="no">
|
|
|
1887 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
1888 </when>
|
|
|
1889 <when value="yes">
|
|
|
1890 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
1891 </when>
|
|
|
1892 </conditional>
|
|
|
1893 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
1894 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
1895 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
1896 <!-- END: 7 samples, no refpairs, entry 7-->
|
|
|
1897 </when>
|
|
|
1898 <when value="yes">
|
|
|
1899 <!-- START: 7 samples, yes refpairs, entry 1-->
|
|
|
1900 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
1901 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
1902 <conditional name="genelist1">
|
|
|
1903 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
1904 <option value="no">Plot whole genome</option>
|
|
|
1905 <option value="yes">Provide restricted gene list</option>
|
|
|
1906 </param>
|
|
|
1907 <when value="no">
|
|
|
1908 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
1909 </when>
|
|
|
1910 <when value="yes">
|
|
|
1911 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
1912 </when>
|
|
|
1913 </conditional>
|
|
|
1914 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
1915 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
1916 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
1917 <!-- END: 7 samples, yes refpairs, entry 1-->
|
|
|
1918 <!-- START: 7 samples, yes refpairs, entry 2-->
|
|
|
1919 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
1920 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
1921 <conditional name="genelist2">
|
|
|
1922 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
1923 <option value="no">Plot whole genome</option>
|
|
|
1924 <option value="yes">Provide restricted gene list</option>
|
|
|
1925 </param>
|
|
|
1926 <when value="no">
|
|
|
1927 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
1928 </when>
|
|
|
1929 <when value="yes">
|
|
|
1930 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
1931 </when>
|
|
|
1932 </conditional>
|
|
|
1933 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
1934 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
1935 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
1936 <!-- END: 7 samples, yes refpairs, entry 2-->
|
|
|
1937 <!-- START: 7 samples, yes refpairs, entry 3-->
|
|
|
1938 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
1939 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
1940 <conditional name="genelist3">
|
|
|
1941 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
1942 <option value="no">Plot whole genome</option>
|
|
|
1943 <option value="yes">Provide restricted gene list</option>
|
|
|
1944 </param>
|
|
|
1945 <when value="no">
|
|
|
1946 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
1947 </when>
|
|
|
1948 <when value="yes">
|
|
|
1949 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
1950 </when>
|
|
|
1951 </conditional>
|
|
|
1952 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
1953 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
1954 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
1955 <!-- END: 7 samples, yes refpairs, entry 3-->
|
|
|
1956 <!-- START: 7 samples, yes refpairs, entry 4-->
|
|
|
1957 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
1958 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
1959 <conditional name="genelist4">
|
|
|
1960 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
1961 <option value="no">Plot whole genome</option>
|
|
|
1962 <option value="yes">Provide restricted gene list</option>
|
|
|
1963 </param>
|
|
|
1964 <when value="no">
|
|
|
1965 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
1966 </when>
|
|
|
1967 <when value="yes">
|
|
|
1968 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
1969 </when>
|
|
|
1970 </conditional>
|
|
|
1971 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
1972 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
1973 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
1974 <!-- END: 7 samples, yes refpairs, entry 4-->
|
|
|
1975 <!-- START: 7 samples, yes refpairs, entry 5-->
|
|
|
1976 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
1977 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
1978 <conditional name="genelist5">
|
|
|
1979 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
1980 <option value="no">Plot whole genome</option>
|
|
|
1981 <option value="yes">Provide restricted gene list</option>
|
|
|
1982 </param>
|
|
|
1983 <when value="no">
|
|
|
1984 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
1985 </when>
|
|
|
1986 <when value="yes">
|
|
|
1987 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
1988 </when>
|
|
|
1989 </conditional>
|
|
|
1990 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
1991 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
1992 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
1993 <!-- END: 7 samples, yes refpairs, entry 5-->
|
|
|
1994 <!-- START: 7 samples, yes refpairs, entry 6-->
|
|
|
1995 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
1996 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
|
|
|
1997 <conditional name="genelist6">
|
|
|
1998 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
1999 <option value="no">Plot whole genome</option>
|
|
|
2000 <option value="yes">Provide restricted gene list</option>
|
|
|
2001 </param>
|
|
|
2002 <when value="no">
|
|
|
2003 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2004 </when>
|
|
|
2005 <when value="yes">
|
|
|
2006 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2007 </when>
|
|
|
2008 </conditional>
|
|
|
2009 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2010 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2011 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2012 <!-- END: 7 samples, yes refpairs, entry 6-->
|
|
|
2013 <!-- START: 7 samples, yes refpairs, entry 7-->
|
|
|
2014 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2015 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
|
|
|
2016 <conditional name="genelist7">
|
|
|
2017 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2018 <option value="no">Plot whole genome</option>
|
|
|
2019 <option value="yes">Provide restricted gene list</option>
|
|
|
2020 </param>
|
|
|
2021 <when value="no">
|
|
|
2022 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2023 </when>
|
|
|
2024 <when value="yes">
|
|
|
2025 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2026 </when>
|
|
|
2027 </conditional>
|
|
|
2028 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2029 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2030 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2031 <!-- END: 7 samples, yes refpairs, entry 7-->
|
|
|
2032 </when>
|
|
|
2033 </conditional>
|
|
|
2034 </when>
|
|
|
2035 <when value="8">
|
|
|
2036 <conditional name="usepair">
|
|
|
2037 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
2038 <option value="no">No</option>
|
|
|
2039 <option value="yes">Yes</option>
|
|
|
2040 </param>
|
|
|
2041 <when value="no">
|
|
|
2042 <!-- START: 8 samples, no refpairs, entry 1-->
|
|
|
2043 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2044 <param type="hidden" name="reffile1" value="na"/>
|
|
|
2045 <conditional name="genelist1">
|
|
|
2046 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2047 <option value="no">Plot whole genome</option>
|
|
|
2048 <option value="yes">Provide restricted gene list</option>
|
|
|
2049 </param>
|
|
|
2050 <when value="no">
|
|
|
2051 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2052 </when>
|
|
|
2053 <when value="yes">
|
|
|
2054 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2055 </when>
|
|
|
2056 </conditional>
|
|
|
2057 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2058 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2059 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2060 <!-- END: 8 samples, no refpairs, entry 1-->
|
|
|
2061 <!-- START: 8 samples, no refpairs, entry 2-->
|
|
|
2062 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2063 <param type="hidden" name="reffile2" value="na"/>
|
|
|
2064 <conditional name="genelist2">
|
|
|
2065 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2066 <option value="no">Plot whole genome</option>
|
|
|
2067 <option value="yes">Provide restricted gene list</option>
|
|
|
2068 </param>
|
|
|
2069 <when value="no">
|
|
|
2070 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2071 </when>
|
|
|
2072 <when value="yes">
|
|
|
2073 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2074 </when>
|
|
|
2075 </conditional>
|
|
|
2076 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2077 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2078 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2079 <!-- END: 8 samples, no refpairs, entry 2-->
|
|
|
2080 <!-- START: 8 samples, no refpairs, entry 3-->
|
|
|
2081 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2082 <param type="hidden" name="reffile3" value="na"/>
|
|
|
2083 <conditional name="genelist3">
|
|
|
2084 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2085 <option value="no">Plot whole genome</option>
|
|
|
2086 <option value="yes">Provide restricted gene list</option>
|
|
|
2087 </param>
|
|
|
2088 <when value="no">
|
|
|
2089 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2090 </when>
|
|
|
2091 <when value="yes">
|
|
|
2092 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2093 </when>
|
|
|
2094 </conditional>
|
|
|
2095 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2096 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2097 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2098 <!-- END: 8 samples, no refpairs, entry 3-->
|
|
|
2099 <!-- START: 8 samples, no refpairs, entry 4-->
|
|
|
2100 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2101 <param type="hidden" name="reffile4" value="na"/>
|
|
|
2102 <conditional name="genelist4">
|
|
|
2103 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2104 <option value="no">Plot whole genome</option>
|
|
|
2105 <option value="yes">Provide restricted gene list</option>
|
|
|
2106 </param>
|
|
|
2107 <when value="no">
|
|
|
2108 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2109 </when>
|
|
|
2110 <when value="yes">
|
|
|
2111 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2112 </when>
|
|
|
2113 </conditional>
|
|
|
2114 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2115 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2116 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2117 <!-- END: 8 samples, no refpairs, entry 4-->
|
|
|
2118 <!-- START: 8 samples, no refpairs, entry 5-->
|
|
|
2119 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2120 <param type="hidden" name="reffile5" value="na"/>
|
|
|
2121 <conditional name="genelist5">
|
|
|
2122 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2123 <option value="no">Plot whole genome</option>
|
|
|
2124 <option value="yes">Provide restricted gene list</option>
|
|
|
2125 </param>
|
|
|
2126 <when value="no">
|
|
|
2127 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2128 </when>
|
|
|
2129 <when value="yes">
|
|
|
2130 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2131 </when>
|
|
|
2132 </conditional>
|
|
|
2133 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2134 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2135 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2136 <!-- END: 8 samples, no refpairs, entry 5-->
|
|
|
2137 <!-- START: 8 samples, no refpairs, entry 6-->
|
|
|
2138 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
2139 <param type="hidden" name="reffile6" value="na"/>
|
|
|
2140 <conditional name="genelist6">
|
|
|
2141 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
2142 <option value="no">Plot whole genome</option>
|
|
|
2143 <option value="yes">Provide restricted gene list</option>
|
|
|
2144 </param>
|
|
|
2145 <when value="no">
|
|
|
2146 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2147 </when>
|
|
|
2148 <when value="yes">
|
|
|
2149 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2150 </when>
|
|
|
2151 </conditional>
|
|
|
2152 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2153 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2154 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2155 <!-- END: 8 samples, no refpairs, entry 6-->
|
|
|
2156 <!-- START: 8 samples, no refpairs, entry 7-->
|
|
|
2157 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2158 <param type="hidden" name="reffile7" value="na"/>
|
|
|
2159 <conditional name="genelist7">
|
|
|
2160 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2161 <option value="no">Plot whole genome</option>
|
|
|
2162 <option value="yes">Provide restricted gene list</option>
|
|
|
2163 </param>
|
|
|
2164 <when value="no">
|
|
|
2165 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2166 </when>
|
|
|
2167 <when value="yes">
|
|
|
2168 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2169 </when>
|
|
|
2170 </conditional>
|
|
|
2171 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2172 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2173 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2174 <!-- END: 8 samples, no refpairs, entry 7-->
|
|
|
2175 <!-- START: 8 samples, no refpairs, entry 8-->
|
|
|
2176 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
2177 <param type="hidden" name="reffile8" value="na"/>
|
|
|
2178 <conditional name="genelist7">
|
|
|
2179 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
2180 <option value="no">Plot whole genome</option>
|
|
|
2181 <option value="yes">Provide restricted gene list</option>
|
|
|
2182 </param>
|
|
|
2183 <when value="no">
|
|
|
2184 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
2185 </when>
|
|
|
2186 <when value="yes">
|
|
|
2187 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
2188 </when>
|
|
|
2189 </conditional>
|
|
|
2190 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
2191 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
2192 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
2193 <!-- END: 8 samples, no refpairs, entry 8-->
|
|
|
2194 </when>
|
|
|
2195 <when value="yes">
|
|
|
2196 <!-- START: 8 samples, yes refpairs, entry 1-->
|
|
|
2197 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2198 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
2199 <conditional name="genelist1">
|
|
|
2200 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2201 <option value="no">Plot whole genome</option>
|
|
|
2202 <option value="yes">Provide restricted gene list</option>
|
|
|
2203 </param>
|
|
|
2204 <when value="no">
|
|
|
2205 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2206 </when>
|
|
|
2207 <when value="yes">
|
|
|
2208 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2209 </when>
|
|
|
2210 </conditional>
|
|
|
2211 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2212 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2213 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2214 <!-- END: 8 samples, yes refpairs, entry 1-->
|
|
|
2215 <!-- START: 8 samples, yes refpairs, entry 2-->
|
|
|
2216 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2217 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
2218 <conditional name="genelist2">
|
|
|
2219 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2220 <option value="no">Plot whole genome</option>
|
|
|
2221 <option value="yes">Provide restricted gene list</option>
|
|
|
2222 </param>
|
|
|
2223 <when value="no">
|
|
|
2224 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2225 </when>
|
|
|
2226 <when value="yes">
|
|
|
2227 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2228 </when>
|
|
|
2229 </conditional>
|
|
|
2230 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2231 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2232 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2233 <!-- END: 8 samples, yes refpairs, entry 2-->
|
|
|
2234 <!-- START: 8 samples, yes refpairs, entry 3-->
|
|
|
2235 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2236 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
2237 <conditional name="genelist3">
|
|
|
2238 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2239 <option value="no">Plot whole genome</option>
|
|
|
2240 <option value="yes">Provide restricted gene list</option>
|
|
|
2241 </param>
|
|
|
2242 <when value="no">
|
|
|
2243 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2244 </when>
|
|
|
2245 <when value="yes">
|
|
|
2246 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2247 </when>
|
|
|
2248 </conditional>
|
|
|
2249 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2250 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2251 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2252 <!-- END: 8 samples, yes refpairs, entry 3-->
|
|
|
2253 <!-- START: 8 samples, yes refpairs, entry 4-->
|
|
|
2254 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2255 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
2256 <conditional name="genelist4">
|
|
|
2257 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2258 <option value="no">Plot whole genome</option>
|
|
|
2259 <option value="yes">Provide restricted gene list</option>
|
|
|
2260 </param>
|
|
|
2261 <when value="no">
|
|
|
2262 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2263 </when>
|
|
|
2264 <when value="yes">
|
|
|
2265 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2266 </when>
|
|
|
2267 </conditional>
|
|
|
2268 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2269 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2270 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2271 <!-- END: 8 samples, yes refpairs, entry 4-->
|
|
|
2272 <!-- START: 8 samples, yes refpairs, entry 5-->
|
|
|
2273 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2274 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
2275 <conditional name="genelist5">
|
|
|
2276 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2277 <option value="no">Plot whole genome</option>
|
|
|
2278 <option value="yes">Provide restricted gene list</option>
|
|
|
2279 </param>
|
|
|
2280 <when value="no">
|
|
|
2281 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2282 </when>
|
|
|
2283 <when value="yes">
|
|
|
2284 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2285 </when>
|
|
|
2286 </conditional>
|
|
|
2287 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2288 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2289 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2290 <!-- END: 8 samples, yes refpairs, entry 5-->
|
|
|
2291 <!-- START: 8 samples, yes refpairs, entry 6-->
|
|
|
2292 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
2293 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
|
|
|
2294 <conditional name="genelist6">
|
|
|
2295 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
2296 <option value="no">Plot whole genome</option>
|
|
|
2297 <option value="yes">Provide restricted gene list</option>
|
|
|
2298 </param>
|
|
|
2299 <when value="no">
|
|
|
2300 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2301 </when>
|
|
|
2302 <when value="yes">
|
|
|
2303 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2304 </when>
|
|
|
2305 </conditional>
|
|
|
2306 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2307 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2308 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2309 <!-- END: 8 samples, yes refpairs, entry 6-->
|
|
|
2310 <!-- START: 8 samples, yes refpairs, entry 7-->
|
|
|
2311 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2312 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
|
|
|
2313 <conditional name="genelist7">
|
|
|
2314 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2315 <option value="no">Plot whole genome</option>
|
|
|
2316 <option value="yes">Provide restricted gene list</option>
|
|
|
2317 </param>
|
|
|
2318 <when value="no">
|
|
|
2319 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2320 </when>
|
|
|
2321 <when value="yes">
|
|
|
2322 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2323 </when>
|
|
|
2324 </conditional>
|
|
|
2325 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2326 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2327 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2328 <!-- END: 8 samples, yes refpairs, entry 7-->
|
|
|
2329 <!-- START: 8 samples, yes refpairs, entry 8-->
|
|
|
2330 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
2331 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
|
|
|
2332 <conditional name="genelist8">
|
|
|
2333 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
2334 <option value="no">Plot whole genome</option>
|
|
|
2335 <option value="yes">Provide restricted gene list</option>
|
|
|
2336 </param>
|
|
|
2337 <when value="no">
|
|
|
2338 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
2339 </when>
|
|
|
2340 <when value="yes">
|
|
|
2341 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
2342 </when>
|
|
|
2343 </conditional>
|
|
|
2344 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
2345 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
2346 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
2347 <!-- END: 8 samples, yes refpairs, entry 8-->
|
|
|
2348 </when>
|
|
|
2349 </conditional>
|
|
|
2350 </when>
|
|
|
2351 <when value="9">
|
|
|
2352 <conditional name="usepair">
|
|
|
2353 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
2354 <option value="no">No</option>
|
|
|
2355 <option value="yes">Yes</option>
|
|
|
2356 </param>
|
|
|
2357 <when value="no">
|
|
|
2358 <!-- START: 9 samples, no refpairs, entry 1-->
|
|
|
2359 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2360 <param type="hidden" name="reffile1" value="na"/>
|
|
|
2361 <conditional name="genelist1">
|
|
|
2362 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2363 <option value="no">Plot whole genome</option>
|
|
|
2364 <option value="yes">Provide restricted gene list</option>
|
|
|
2365 </param>
|
|
|
2366 <when value="no">
|
|
|
2367 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2368 </when>
|
|
|
2369 <when value="yes">
|
|
|
2370 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2371 </when>
|
|
|
2372 </conditional>
|
|
|
2373 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2374 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2375 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2376 <!-- END: 9 samples, no refpairs, entry 1-->
|
|
|
2377 <!-- START: 9 samples, no refpairs, entry 2-->
|
|
|
2378 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2379 <param type="hidden" name="reffile2" value="na"/>
|
|
|
2380 <conditional name="genelist2">
|
|
|
2381 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2382 <option value="no">Plot whole genome</option>
|
|
|
2383 <option value="yes">Provide restricted gene list</option>
|
|
|
2384 </param>
|
|
|
2385 <when value="no">
|
|
|
2386 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2387 </when>
|
|
|
2388 <when value="yes">
|
|
|
2389 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2390 </when>
|
|
|
2391 </conditional>
|
|
|
2392 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2393 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2394 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2395 <!-- END: 9 samples, no refpairs, entry 2-->
|
|
|
2396 <!-- START: 9 samples, no refpairs, entry 3-->
|
|
|
2397 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2398 <param type="hidden" name="reffile3" value="na"/>
|
|
|
2399 <conditional name="genelist3">
|
|
|
2400 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2401 <option value="no">Plot whole genome</option>
|
|
|
2402 <option value="yes">Provide restricted gene list</option>
|
|
|
2403 </param>
|
|
|
2404 <when value="no">
|
|
|
2405 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2406 </when>
|
|
|
2407 <when value="yes">
|
|
|
2408 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2409 </when>
|
|
|
2410 </conditional>
|
|
|
2411 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2412 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2413 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2414 <!-- END: 9 samples, no refpairs, entry 3-->
|
|
|
2415 <!-- START: 9 samples, no refpairs, entry 4-->
|
|
|
2416 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2417 <param type="hidden" name="reffile4" value="na"/>
|
|
|
2418 <conditional name="genelist4">
|
|
|
2419 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2420 <option value="no">Plot whole genome</option>
|
|
|
2421 <option value="yes">Provide restricted gene list</option>
|
|
|
2422 </param>
|
|
|
2423 <when value="no">
|
|
|
2424 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2425 </when>
|
|
|
2426 <when value="yes">
|
|
|
2427 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2428 </when>
|
|
|
2429 </conditional>
|
|
|
2430 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2431 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2432 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2433 <!-- END: 9 samples, no refpairs, entry 4-->
|
|
|
2434 <!-- START: 9 samples, no refpairs, entry 5-->
|
|
|
2435 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2436 <param type="hidden" name="reffile5" value="na"/>
|
|
|
2437 <conditional name="genelist5">
|
|
|
2438 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2439 <option value="no">Plot whole genome</option>
|
|
|
2440 <option value="yes">Provide restricted gene list</option>
|
|
|
2441 </param>
|
|
|
2442 <when value="no">
|
|
|
2443 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2444 </when>
|
|
|
2445 <when value="yes">
|
|
|
2446 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2447 </when>
|
|
|
2448 </conditional>
|
|
|
2449 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2450 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2451 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2452 <!-- END: 9 samples, no refpairs, entry 5-->
|
|
|
2453 <!-- START: 9 samples, no refpairs, entry 6-->
|
|
|
2454 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
2455 <param type="hidden" name="reffile6" value="na"/>
|
|
|
2456 <conditional name="genelist6">
|
|
|
2457 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
2458 <option value="no">Plot whole genome</option>
|
|
|
2459 <option value="yes">Provide restricted gene list</option>
|
|
|
2460 </param>
|
|
|
2461 <when value="no">
|
|
|
2462 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2463 </when>
|
|
|
2464 <when value="yes">
|
|
|
2465 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2466 </when>
|
|
|
2467 </conditional>
|
|
|
2468 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2469 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2470 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2471 <!-- END: 9 samples, no refpairs, entry 6-->
|
|
|
2472 <!-- START: 9 samples, no refpairs, entry 7-->
|
|
|
2473 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2474 <param type="hidden" name="reffile7" value="na"/>
|
|
|
2475 <conditional name="genelist7">
|
|
|
2476 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2477 <option value="no">Plot whole genome</option>
|
|
|
2478 <option value="yes">Provide restricted gene list</option>
|
|
|
2479 </param>
|
|
|
2480 <when value="no">
|
|
|
2481 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2482 </when>
|
|
|
2483 <when value="yes">
|
|
|
2484 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2485 </when>
|
|
|
2486 </conditional>
|
|
|
2487 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2488 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2489 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2490 <!-- END: 9 samples, no refpairs, entry 7-->
|
|
|
2491 <!-- START: 9 samples, no refpairs, entry 8-->
|
|
|
2492 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
2493 <param type="hidden" name="reffile8" value="na"/>
|
|
|
2494 <conditional name="genelist8">
|
|
|
2495 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
2496 <option value="no">Plot whole genome</option>
|
|
|
2497 <option value="yes">Provide restricted gene list</option>
|
|
|
2498 </param>
|
|
|
2499 <when value="no">
|
|
|
2500 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
2501 </when>
|
|
|
2502 <when value="yes">
|
|
|
2503 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
2504 </when>
|
|
|
2505 </conditional>
|
|
|
2506 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
2507 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
2508 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
2509 <!-- END: 9 samples, no refpairs, entry 8-->
|
|
|
2510 <!-- START: 9 samples, no refpairs, entry 9-->
|
|
|
2511 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
|
|
|
2512 <param type="hidden" name="reffile9" value="na"/>
|
|
|
2513 <conditional name="genelist9">
|
|
|
2514 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
|
|
|
2515 <option value="no">Plot whole genome</option>
|
|
|
2516 <option value="yes">Provide restricted gene list</option>
|
|
|
2517 </param>
|
|
|
2518 <when value="no">
|
|
|
2519 <param type="hidden" name="genelist9" value="-1"/>
|
|
|
2520 </when>
|
|
|
2521 <when value="yes">
|
|
|
2522 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
|
|
|
2523 </when>
|
|
|
2524 </conditional>
|
|
|
2525 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
|
|
|
2526 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
|
|
|
2527 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
|
|
|
2528 <!-- END: 9 samples, no refpairs, entry 9-->
|
|
|
2529 </when>
|
|
|
2530 <when value="yes">
|
|
|
2531 <!-- START: 9 samples, yes refpairs, entry 1-->
|
|
|
2532 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2533 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
2534 <conditional name="genelist1">
|
|
|
2535 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2536 <option value="no">Plot whole genome</option>
|
|
|
2537 <option value="yes">Provide restricted gene list</option>
|
|
|
2538 </param>
|
|
|
2539 <when value="no">
|
|
|
2540 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2541 </when>
|
|
|
2542 <when value="yes">
|
|
|
2543 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2544 </when>
|
|
|
2545 </conditional>
|
|
|
2546 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2547 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2548 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2549 <!-- END: 9 samples, yes refpairs, entry 1-->
|
|
|
2550 <!-- START: 9 samples, yes refpairs, entry 2-->
|
|
|
2551 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2552 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
2553 <conditional name="genelist2">
|
|
|
2554 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2555 <option value="no">Plot whole genome</option>
|
|
|
2556 <option value="yes">Provide restricted gene list</option>
|
|
|
2557 </param>
|
|
|
2558 <when value="no">
|
|
|
2559 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2560 </when>
|
|
|
2561 <when value="yes">
|
|
|
2562 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2563 </when>
|
|
|
2564 </conditional>
|
|
|
2565 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2566 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2567 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2568 <!-- END: 9 samples, yes refpairs, entry 2-->
|
|
|
2569 <!-- START: 9 samples, yes refpairs, entry 3-->
|
|
|
2570 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2571 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
2572 <conditional name="genelist3">
|
|
|
2573 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2574 <option value="no">Plot whole genome</option>
|
|
|
2575 <option value="yes">Provide restricted gene list</option>
|
|
|
2576 </param>
|
|
|
2577 <when value="no">
|
|
|
2578 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2579 </when>
|
|
|
2580 <when value="yes">
|
|
|
2581 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2582 </when>
|
|
|
2583 </conditional>
|
|
|
2584 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2585 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2586 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2587 <!-- END: 9 samples, yes refpairs, entry 3-->
|
|
|
2588 <!-- START: 9 samples, yes refpairs, entry 4-->
|
|
|
2589 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2590 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
2591 <conditional name="genelist4">
|
|
|
2592 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2593 <option value="no">Plot whole genome</option>
|
|
|
2594 <option value="yes">Provide restricted gene list</option>
|
|
|
2595 </param>
|
|
|
2596 <when value="no">
|
|
|
2597 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2598 </when>
|
|
|
2599 <when value="yes">
|
|
|
2600 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2601 </when>
|
|
|
2602 </conditional>
|
|
|
2603 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2604 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2605 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2606 <!-- END: 9 samples, yes refpairs, entry 4-->
|
|
|
2607 <!-- START: 9 samples, yes refpairs, entry 5-->
|
|
|
2608 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2609 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
2610 <conditional name="genelist5">
|
|
|
2611 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2612 <option value="no">Plot whole genome</option>
|
|
|
2613 <option value="yes">Provide restricted gene list</option>
|
|
|
2614 </param>
|
|
|
2615 <when value="no">
|
|
|
2616 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2617 </when>
|
|
|
2618 <when value="yes">
|
|
|
2619 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2620 </when>
|
|
|
2621 </conditional>
|
|
|
2622 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2623 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2624 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2625 <!-- END: 9 samples, yes refpairs, entry 5-->
|
|
|
2626 <!-- START: 9 samples, yes refpairs, entry 6-->
|
|
|
2627 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
2628 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
|
|
|
2629 <conditional name="genelist6">
|
|
|
2630 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
2631 <option value="no">Plot whole genome</option>
|
|
|
2632 <option value="yes">Provide restricted gene list</option>
|
|
|
2633 </param>
|
|
|
2634 <when value="no">
|
|
|
2635 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2636 </when>
|
|
|
2637 <when value="yes">
|
|
|
2638 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2639 </when>
|
|
|
2640 </conditional>
|
|
|
2641 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2642 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2643 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2644 <!-- END: 9 samples, yes refpairs, entry 6-->
|
|
|
2645 <!-- START: 9 samples, yes refpairs, entry 7-->
|
|
|
2646 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2647 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
|
|
|
2648 <conditional name="genelist7">
|
|
|
2649 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2650 <option value="no">Plot whole genome</option>
|
|
|
2651 <option value="yes">Provide restricted gene list</option>
|
|
|
2652 </param>
|
|
|
2653 <when value="no">
|
|
|
2654 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2655 </when>
|
|
|
2656 <when value="yes">
|
|
|
2657 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2658 </when>
|
|
|
2659 </conditional>
|
|
|
2660 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2661 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2662 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2663 <!-- END: 9 samples, yes refpairs, entry 7-->
|
|
|
2664 <!-- START: 9 samples, yes refpairs, entry 8-->
|
|
|
2665 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
2666 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
|
|
|
2667 <conditional name="genelist8">
|
|
|
2668 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
2669 <option value="no">Plot whole genome</option>
|
|
|
2670 <option value="yes">Provide restricted gene list</option>
|
|
|
2671 </param>
|
|
|
2672 <when value="no">
|
|
|
2673 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
2674 </when>
|
|
|
2675 <when value="yes">
|
|
|
2676 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
2677 </when>
|
|
|
2678 </conditional>
|
|
|
2679 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
2680 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
2681 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
2682 <!-- END: 9 samples, yes refpairs, entry 8-->
|
|
|
2683 <!-- START: 9 samples, yes refpairs, entry 9-->
|
|
|
2684 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
|
|
|
2685 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
|
|
|
2686 <conditional name="genelist9">
|
|
|
2687 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
|
|
|
2688 <option value="no">Plot whole genome</option>
|
|
|
2689 <option value="yes">Provide restricted gene list</option>
|
|
|
2690 </param>
|
|
|
2691 <when value="no">
|
|
|
2692 <param type="hidden" name="genelist9" value="-1"/>
|
|
|
2693 </when>
|
|
|
2694 <when value="yes">
|
|
|
2695 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
|
|
|
2696 </when>
|
|
|
2697 </conditional>
|
|
|
2698 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
|
|
|
2699 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
|
|
|
2700 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
|
|
|
2701 <!-- END: 9 samples, yes refpairs, entry 9-->
|
|
|
2702 </when>
|
|
|
2703 </conditional>
|
|
|
2704 </when>
|
|
|
2705 <when value="10">
|
|
|
2706 <conditional name="usepair">
|
|
|
2707 <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
|
|
|
2708 <option value="no">No</option>
|
|
|
2709 <option value="yes">Yes</option>
|
|
|
2710 </param>
|
|
|
2711 <when value="no">
|
|
|
2712 <!-- START: 10 samples, no refpairs, entry 1-->
|
|
|
2713 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2714 <param type="hidden" name="reffile1" value="na"/>
|
|
|
2715 <conditional name="genelist1">
|
|
|
2716 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2717 <option value="no">Plot whole genome</option>
|
|
|
2718 <option value="yes">Provide restricted gene list</option>
|
|
|
2719 </param>
|
|
|
2720 <when value="no">
|
|
|
2721 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2722 </when>
|
|
|
2723 <when value="yes">
|
|
|
2724 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2725 </when>
|
|
|
2726 </conditional>
|
|
|
2727 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2728 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2729 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2730 <!-- END: 10 samples, no refpairs, entry 1-->
|
|
|
2731 <!-- START: 10 samples, no refpairs, entry 2-->
|
|
|
2732 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2733 <param type="hidden" name="reffile2" value="na"/>
|
|
|
2734 <conditional name="genelist2">
|
|
|
2735 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2736 <option value="no">Plot whole genome</option>
|
|
|
2737 <option value="yes">Provide restricted gene list</option>
|
|
|
2738 </param>
|
|
|
2739 <when value="no">
|
|
|
2740 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2741 </when>
|
|
|
2742 <when value="yes">
|
|
|
2743 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2744 </when>
|
|
|
2745 </conditional>
|
|
|
2746 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2747 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2748 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2749 <!-- END: 10 samples, no refpairs, entry 2-->
|
|
|
2750 <!-- START: 10 samples, no refpairs, entry 3-->
|
|
|
2751 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2752 <param type="hidden" name="reffile3" value="na"/>
|
|
|
2753 <conditional name="genelist3">
|
|
|
2754 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2755 <option value="no">Plot whole genome</option>
|
|
|
2756 <option value="yes">Provide restricted gene list</option>
|
|
|
2757 </param>
|
|
|
2758 <when value="no">
|
|
|
2759 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2760 </when>
|
|
|
2761 <when value="yes">
|
|
|
2762 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2763 </when>
|
|
|
2764 </conditional>
|
|
|
2765 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2766 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2767 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2768 <!-- END: 10 samples, no refpairs, entry 3-->
|
|
|
2769 <!-- START: 10 samples, no refpairs, entry 4-->
|
|
|
2770 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2771 <param type="hidden" name="reffile4" value="na"/>
|
|
|
2772 <conditional name="genelist4">
|
|
|
2773 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2774 <option value="no">Plot whole genome</option>
|
|
|
2775 <option value="yes">Provide restricted gene list</option>
|
|
|
2776 </param>
|
|
|
2777 <when value="no">
|
|
|
2778 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2779 </when>
|
|
|
2780 <when value="yes">
|
|
|
2781 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2782 </when>
|
|
|
2783 </conditional>
|
|
|
2784 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2785 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2786 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2787 <!-- END: 10 samples, no refpairs, entry 4-->
|
|
|
2788 <!-- START: 10 samples, no refpairs, entry 5-->
|
|
|
2789 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2790 <param type="hidden" name="reffile5" value="na"/>
|
|
|
2791 <conditional name="genelist5">
|
|
|
2792 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2793 <option value="no">Plot whole genome</option>
|
|
|
2794 <option value="yes">Provide restricted gene list</option>
|
|
|
2795 </param>
|
|
|
2796 <when value="no">
|
|
|
2797 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2798 </when>
|
|
|
2799 <when value="yes">
|
|
|
2800 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2801 </when>
|
|
|
2802 </conditional>
|
|
|
2803 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2804 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2805 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2806 <!-- END: 10 samples, no refpairs, entry 5-->
|
|
|
2807 <!-- START: 10 samples, no refpairs, entry 6-->
|
|
|
2808 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
2809 <param type="hidden" name="reffile6" value="na"/>
|
|
|
2810 <conditional name="genelist6">
|
|
|
2811 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
2812 <option value="no">Plot whole genome</option>
|
|
|
2813 <option value="yes">Provide restricted gene list</option>
|
|
|
2814 </param>
|
|
|
2815 <when value="no">
|
|
|
2816 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
2817 </when>
|
|
|
2818 <when value="yes">
|
|
|
2819 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
2820 </when>
|
|
|
2821 </conditional>
|
|
|
2822 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
2823 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
2824 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
2825 <!-- END: 10 samples, no refpairs, entry 6-->
|
|
|
2826 <!-- START: 10 samples, no refpairs, entry 7-->
|
|
|
2827 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
2828 <param type="hidden" name="reffile7" value="na"/>
|
|
|
2829 <conditional name="genelist7">
|
|
|
2830 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
2831 <option value="no">Plot whole genome</option>
|
|
|
2832 <option value="yes">Provide restricted gene list</option>
|
|
|
2833 </param>
|
|
|
2834 <when value="no">
|
|
|
2835 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
2836 </when>
|
|
|
2837 <when value="yes">
|
|
|
2838 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
2839 </when>
|
|
|
2840 </conditional>
|
|
|
2841 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
2842 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
2843 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
2844 <!-- END: 10 samples, no refpairs, entry 7-->
|
|
|
2845 <!-- START: 10 samples, no refpairs, entry 8-->
|
|
|
2846 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
2847 <param type="hidden" name="reffile8" value="na"/>
|
|
|
2848 <conditional name="genelist8">
|
|
|
2849 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
2850 <option value="no">Plot whole genome</option>
|
|
|
2851 <option value="yes">Provide restricted gene list</option>
|
|
|
2852 </param>
|
|
|
2853 <when value="no">
|
|
|
2854 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
2855 </when>
|
|
|
2856 <when value="yes">
|
|
|
2857 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
2858 </when>
|
|
|
2859 </conditional>
|
|
|
2860 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
2861 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
2862 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
2863 <!-- END: 10 samples, no refpairs, entry 8-->
|
|
|
2864 <!-- START: 10 samples, no refpairs, entry 9-->
|
|
|
2865 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
|
|
|
2866 <param type="hidden" name="reffile9" value="na"/>
|
|
|
2867 <conditional name="genelist9">
|
|
|
2868 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
|
|
|
2869 <option value="no">Plot whole genome</option>
|
|
|
2870 <option value="yes">Provide restricted gene list</option>
|
|
|
2871 </param>
|
|
|
2872 <when value="no">
|
|
|
2873 <param type="hidden" name="genelist9" value="-1"/>
|
|
|
2874 </when>
|
|
|
2875 <when value="yes">
|
|
|
2876 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
|
|
|
2877 </when>
|
|
|
2878 </conditional>
|
|
|
2879 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
|
|
|
2880 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
|
|
|
2881 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
|
|
|
2882 <!-- END: 10 samples, no refpairs, entry 9-->
|
|
|
2883 <!-- START: 10 samples, no refpairs, entry 10-->
|
|
|
2884 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
|
|
|
2885 <param type="hidden" name="reffile10" value="na"/>
|
|
|
2886 <conditional name="genelist10">
|
|
|
2887 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
|
|
|
2888 <option value="no">Plot whole genome</option>
|
|
|
2889 <option value="yes">Provide restricted gene list</option>
|
|
|
2890 </param>
|
|
|
2891 <when value="no">
|
|
|
2892 <param type="hidden" name="genelist10" value="-1"/>
|
|
|
2893 </when>
|
|
|
2894 <when value="yes">
|
|
|
2895 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
|
|
|
2896 </when>
|
|
|
2897 </conditional>
|
|
|
2898 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
|
|
|
2899 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
|
|
|
2900 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
|
|
|
2901 <!-- END: 10 samples, no refpairs, entry 10-->
|
|
|
2902 </when>
|
|
|
2903 <when value="yes">
|
|
|
2904 <!-- START: 10 samples, yes refpairs, entry 1-->
|
|
|
2905 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
|
|
|
2906 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
|
|
|
2907 <conditional name="genelist1">
|
|
|
2908 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
|
|
|
2909 <option value="no">Plot whole genome</option>
|
|
|
2910 <option value="yes">Provide restricted gene list</option>
|
|
|
2911 </param>
|
|
|
2912 <when value="no">
|
|
|
2913 <param type="hidden" name="genelist1" value="-1"/>
|
|
|
2914 </when>
|
|
|
2915 <when value="yes">
|
|
|
2916 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
|
|
|
2917 </when>
|
|
|
2918 </conditional>
|
|
|
2919 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
|
|
|
2920 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
|
|
|
2921 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
|
|
|
2922 <!-- END: 10 samples, yes refpairs, entry 1-->
|
|
|
2923 <!-- START: 10 samples, yes refpairs, entry 2-->
|
|
|
2924 <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/>
|
|
|
2925 <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/>
|
|
|
2926 <conditional name="genelist2">
|
|
|
2927 <param type="select" name="usegenelist2" label="Sample 2: Gene list">
|
|
|
2928 <option value="no">Plot whole genome</option>
|
|
|
2929 <option value="yes">Provide restricted gene list</option>
|
|
|
2930 </param>
|
|
|
2931 <when value="no">
|
|
|
2932 <param type="hidden" name="genelist2" value="-1"/>
|
|
|
2933 </when>
|
|
|
2934 <when value="yes">
|
|
|
2935 <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/>
|
|
|
2936 </when>
|
|
|
2937 </conditional>
|
|
|
2938 <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/>
|
|
|
2939 <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>
|
|
|
2940 <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/>
|
|
|
2941 <!-- END: 10 samples, yes refpairs, entry 2-->
|
|
|
2942 <!-- START: 10 samples, yes refpairs, entry 3-->
|
|
|
2943 <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/>
|
|
|
2944 <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/>
|
|
|
2945 <conditional name="genelist3">
|
|
|
2946 <param type="select" name="usegenelist3" label="Sample 3: Gene list">
|
|
|
2947 <option value="no">Plot whole genome</option>
|
|
|
2948 <option value="yes">Provide restricted gene list</option>
|
|
|
2949 </param>
|
|
|
2950 <when value="no">
|
|
|
2951 <param type="hidden" name="genelist3" value="-1"/>
|
|
|
2952 </when>
|
|
|
2953 <when value="yes">
|
|
|
2954 <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/>
|
|
|
2955 </when>
|
|
|
2956 </conditional>
|
|
|
2957 <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/>
|
|
|
2958 <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>
|
|
|
2959 <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/>
|
|
|
2960 <!-- END: 10 samples, yes refpairs, entry 3-->
|
|
|
2961 <!-- START: 10 samples, yes refpairs, entry 4-->
|
|
|
2962 <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/>
|
|
|
2963 <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/>
|
|
|
2964 <conditional name="genelist4">
|
|
|
2965 <param type="select" name="usegenelist4" label="Sample 4: Gene list">
|
|
|
2966 <option value="no">Plot whole genome</option>
|
|
|
2967 <option value="yes">Provide restricted gene list</option>
|
|
|
2968 </param>
|
|
|
2969 <when value="no">
|
|
|
2970 <param type="hidden" name="genelist4" value="-1"/>
|
|
|
2971 </when>
|
|
|
2972 <when value="yes">
|
|
|
2973 <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/>
|
|
|
2974 </when>
|
|
|
2975 </conditional>
|
|
|
2976 <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/>
|
|
|
2977 <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>
|
|
|
2978 <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/>
|
|
|
2979 <!-- END: 10 samples, yes refpairs, entry 4-->
|
|
|
2980 <!-- START: 10 samples, yes refpairs, entry 5-->
|
|
|
2981 <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/>
|
|
|
2982 <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/>
|
|
|
2983 <conditional name="genelist5">
|
|
|
2984 <param type="select" name="usegenelist5" label="Sample 5: Gene list">
|
|
|
2985 <option value="no">Plot whole genome</option>
|
|
|
2986 <option value="yes">Provide restricted gene list</option>
|
|
|
2987 </param>
|
|
|
2988 <when value="no">
|
|
|
2989 <param type="hidden" name="genelist5" value="-1"/>
|
|
|
2990 </when>
|
|
|
2991 <when value="yes">
|
|
|
2992 <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/>
|
|
|
2993 </when>
|
|
|
2994 </conditional>
|
|
|
2995 <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/>
|
|
|
2996 <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>
|
|
|
2997 <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>
|
|
|
2998 <!-- END: 10 samples, yes refpairs, entry 5-->
|
|
|
2999 <!-- START: 10 samples, yes refpairs, entry 6-->
|
|
|
3000 <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/>
|
|
|
3001 <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/>
|
|
|
3002 <conditional name="genelist6">
|
|
|
3003 <param type="select" name="usegenelist6" label="Sample 6: Gene list">
|
|
|
3004 <option value="no">Plot whole genome</option>
|
|
|
3005 <option value="yes">Provide restricted gene list</option>
|
|
|
3006 </param>
|
|
|
3007 <when value="no">
|
|
|
3008 <param type="hidden" name="genelist6" value="-1"/>
|
|
|
3009 </when>
|
|
|
3010 <when value="yes">
|
|
|
3011 <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/>
|
|
|
3012 </when>
|
|
|
3013 </conditional>
|
|
|
3014 <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/>
|
|
|
3015 <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>
|
|
|
3016 <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/>
|
|
|
3017 <!-- END: 10 samples, yes refpairs, entry 6-->
|
|
|
3018 <!-- START: 10 samples, yes refpairs, entry 7-->
|
|
|
3019 <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/>
|
|
|
3020 <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/>
|
|
|
3021 <conditional name="genelist7">
|
|
|
3022 <param type="select" name="usegenelist7" label="Sample 7: Gene list">
|
|
|
3023 <option value="no">Plot whole genome</option>
|
|
|
3024 <option value="yes">Provide restricted gene list</option>
|
|
|
3025 </param>
|
|
|
3026 <when value="no">
|
|
|
3027 <param type="hidden" name="genelist7" value="-1"/>
|
|
|
3028 </when>
|
|
|
3029 <when value="yes">
|
|
|
3030 <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/>
|
|
|
3031 </when>
|
|
|
3032 </conditional>
|
|
|
3033 <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/>
|
|
|
3034 <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>
|
|
|
3035 <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/>
|
|
|
3036 <!-- END: 10 samples, yes refpairs, entry 7-->
|
|
|
3037 <!-- START: 10 samples, yes refpairs, entry 8-->
|
|
|
3038 <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/>
|
|
|
3039 <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/>
|
|
|
3040 <conditional name="genelist8">
|
|
|
3041 <param type="select" name="usegenelist8" label="Sample 8: Gene list">
|
|
|
3042 <option value="no">Plot whole genome</option>
|
|
|
3043 <option value="yes">Provide restricted gene list</option>
|
|
|
3044 </param>
|
|
|
3045 <when value="no">
|
|
|
3046 <param type="hidden" name="genelist8" value="-1"/>
|
|
|
3047 </when>
|
|
|
3048 <when value="yes">
|
|
|
3049 <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/>
|
|
|
3050 </when>
|
|
|
3051 </conditional>
|
|
|
3052 <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/>
|
|
|
3053 <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>
|
|
|
3054 <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>
|
|
|
3055 <!-- END: 10 samples, yes refpairs, entry 8-->
|
|
|
3056 <!-- START: 10 samples, yes refpairs, entry 9-->
|
|
|
3057 <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/>
|
|
|
3058 <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/>
|
|
|
3059 <conditional name="genelist9">
|
|
|
3060 <param type="select" name="usegenelist9" label="Sample 9: Gene list">
|
|
|
3061 <option value="no">Plot whole genome</option>
|
|
|
3062 <option value="yes">Provide restricted gene list</option>
|
|
|
3063 </param>
|
|
|
3064 <when value="no">
|
|
|
3065 <param type="hidden" name="genelist9" value="-1"/>
|
|
|
3066 </when>
|
|
|
3067 <when value="yes">
|
|
|
3068 <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/>
|
|
|
3069 </when>
|
|
|
3070 </conditional>
|
|
|
3071 <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/>
|
|
|
3072 <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>
|
|
|
3073 <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/>
|
|
|
3074 <!-- END: 10 samples, yes refpairs, entry 9-->
|
|
|
3075 <!-- START: 10 samples, yes refpairs, entry 10-->
|
|
|
3076 <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/>
|
|
|
3077 <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/>
|
|
|
3078 <conditional name="genelist10">
|
|
|
3079 <param type="select" name="usegenelist10" label="Sample 10: Gene list">
|
|
|
3080 <option value="no">Plot whole genome</option>
|
|
|
3081 <option value="yes">Provide restricted gene list</option>
|
|
|
3082 </param>
|
|
|
3083 <when value="no">
|
|
|
3084 <param type="hidden" name="genelist10" value="-1"/>
|
|
|
3085 </when>
|
|
|
3086 <when value="yes">
|
|
|
3087 <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/>
|
|
|
3088 </when>
|
|
|
3089 </conditional>
|
|
|
3090 <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/>
|
|
|
3091 <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>
|
|
|
3092 <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/>
|
|
|
3093 <!-- END: 10 samples, yes refpairs, entry 10-->
|
|
|
3094 </when>
|
|
|
3095 </conditional>
|
|
|
3096 </when>
|
|
|
3097 </conditional>
|
|
|
3098
|
|
|
3099
|
|
|
3100
|
|
|
3101 <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
|
|
|
3102 <option value="ensembl">Ensembl</option>
|
|
|
3103 <option value="refseq">RefSeq</option>
|
|
|
3104 </param>
|
|
|
3105 <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/>
|
|
|
3106 <conditional name="GO">
|
|
|
3107 <param type="select" name="gene_order" label="Gene order algorithm">
|
|
|
3108 <option value="total">Overall enrichment of the 1st profile</option>
|
|
|
3109 <option value="hc">Hierarchical clustering</option>
|
|
|
3110 <option value="max">Peak value of the 1st profile</option>
|
|
|
3111 <option value="prod">Product of all profiles on the same region</option>
|
|
|
3112 <option value="diff">Difference between the 1st and 2nd profiles</option>
|
|
|
3113 <option value="km">K-means clustering</option>
|
|
|
3114 <option value="none">No ranking algorithm applied. Use order in gene list.</option>
|
|
|
3115 </param>
|
|
|
3116 <when value="km">
|
|
|
3117 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
|
|
|
3118 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
|
|
|
3119 <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
|
|
|
3120 </when>
|
|
|
3121 <when value="total">
|
|
|
3122 <param type="hidden" name="KNC" value="NA" />
|
|
|
3123 <param type="hidden" name="MIT" value="NA" />
|
|
|
3124 <param type="hidden" name="NRS" value="NA" />
|
|
|
3125 </when>
|
|
|
3126 <when value="hc">
|
|
|
3127 <param type="hidden" name="KNC" value="NA" />
|
|
|
3128 <param type="hidden" name="MIT" value="NA" />
|
|
|
3129 <param type="hidden" name="NRS" value="NA" />
|
|
|
3130 </when>
|
|
|
3131 <when value="max">
|
|
|
3132 <param type="hidden" name="KNC" value="NA" />
|
|
|
3133 <param type="hidden" name="MIT" value="NA" />
|
|
|
3134 <param type="hidden" name="NRS" value="NA" />
|
|
|
3135 </when>
|
|
|
3136 <when value="prod">
|
|
|
3137 <param type="hidden" name="KNC" value="NA" />
|
|
|
3138 <param type="hidden" name="MIT" value="NA" />
|
|
|
3139 <param type="hidden" name="NRS" value="NA" />
|
|
|
3140 </when>
|
|
|
3141 <when value="diff">
|
|
|
3142 <param type="hidden" name="KNC" value="NA" />
|
|
|
3143 <param type="hidden" name="MIT" value="NA" />
|
|
|
3144 <param type="hidden" name="NRS" value="NA" />
|
|
|
3145 </when>
|
|
|
3146 <when value="none">
|
|
|
3147 <param type="hidden" name="KNC" value="NA" />
|
|
|
3148 <param type="hidden" name="MIT" value="NA" />
|
|
|
3149 <param type="hidden" name="NRS" value="NA" />
|
|
|
3150 </when>
|
|
|
3151 </conditional>
|
|
|
3152 <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/>
|
|
|
3153 <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/>
|
|
|
3154 <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
|
|
|
3155 <option value="1">Yes</option>
|
|
|
3156 <option value="0">No</option>
|
|
|
3157 </param>
|
|
|
3158
|
|
|
3159 <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/>
|
|
|
3160 <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/>
|
|
|
3161 <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
|
|
|
3162 <option value="1">No</option>
|
|
|
3163 <option value="3">Slightly</option>
|
|
|
3164 <option value="5">Somewhat</option>
|
|
|
3165 <option value="9">Quite</option>
|
|
|
3166 <option value="13">Super</option>
|
|
|
3167 </param>
|
|
|
3168 <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/>
|
|
|
3169 <!--
|
|
|
3170 -->
|
|
|
3171 </inputs>
|
|
|
3172
|
|
|
3173 <help>---TEST---</help>
|
|
|
3174 <outputs>
|
|
|
3175 <data format="pdf" name="out_avg_png" />
|
|
|
3176 <data format="pdf" name="out_hm_png" />
|
|
|
3177 <data format="zip" name="out_zip"/>
|
|
|
3178 </outputs>
|
|
|
3179 </tool>
|
