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