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1 <?xml version="1.0"?>
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2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.0">
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3 <description>tabular files from a cummeRbund database</description>
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4 <command interpreter="python"><![CDATA[
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5 cummerbund_to_tabular.py --file ${input_database}
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6 ${cds_count} ${cds_diff} ${cds_exp_diff} ${cds_fpkm} ${cds_rg}
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7 ${gene_exp_diff} ${genes_count} ${genes_fpkm} ${gene_rg} ${isoform_exp_diff}
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8 ${isoform_count} ${isoform_fpkm} ${isoform_rg} ${promoters_diff} ${read_groups}
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9 ${run_info} ${splicing_diff} ${tss_group_exp} ${tss_count_tracking} ${tss_fpkm}
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10 ${tss_rg} ${var_model}
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11 ]]></command>
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12 <inputs>
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13 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
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14 <param type="boolean" name="cds_count" truevalue="--tables cds_count" falsevalue="" label="CDS count tracking" />
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15 <param type="boolean" name="cds_diff" truevalue="--tables cds_diff" falsevalue="" label="CDS overloading diffential expression testing" />
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16 <param type="boolean" name="cds_exp_diff" truevalue="--tables cds_exp_diff" falsevalue="" label="CDS FPKM differential expression testing" />
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17 <param type="boolean" name="cds_fpkm" truevalue="--tables cds_fpkm" falsevalue="" label="CDS FPKM tracking" />
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18 <param type="boolean" name="cds_rg" truevalue="--tables cds_rg" falsevalue="" label="CDS read groups" />
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19 <param type="boolean" name="gene_exp_diff" truevalue="--tables gene_exp_diff" falsevalue="" label="gene differential expression testing" />
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20 <param type="boolean" name="genes_count" truevalue="--tables genes_count" falsevalue="" label="gene count tracking" />
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21 <param type="boolean" name="genes_fpkm" truevalue="--tables genes_fpkm" falsevalue="" label="gene FPKM tracking" />
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22 <param type="boolean" name="gene_rg" truevalue="--tables gene_rg" falsevalue="" label="gene read groups" />
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23 <param type="boolean" name="isoform_exp_diff" truevalue="--tables isoform_exp_diff" falsevalue="" label="transcript differential expression testing" />
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24 <param type="boolean" name="isoform_count" truevalue="--tables isoform_count" falsevalue="" label="transcript count tracking" />
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25 <param type="boolean" name="isoform_fpkm" truevalue="--tables isoform_fpkm" falsevalue="" label="transcript FPKM tracking" />
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26 <param type="boolean" name="isoform_rg" truevalue="--tables isoform_rg" falsevalue="" label="transcript read groups" />
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27 <param type="boolean" name="promoters_diff" truevalue="--tables promoters_diff" falsevalue="" label="promoter differential testing" />
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28 <param type="boolean" name="read_groups" truevalue="--tables read_groups" falsevalue="" label="Read Groups" />
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29 <param type="boolean" name="run_info" truevalue="--tables run_info" falsevalue="" label="Run details" />
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30 <param type="boolean" name="splicing_diff" truevalue="--tables splicing_diff" falsevalue="" label="splicing differential expression testing" />
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31 <param type="boolean" name="tss_group_exp" truevalue="--tables tss_group_exp" falsevalue="" label="TSS groups differential expression testing" />
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32 <param type="boolean" name="tss_count_tracking" truevalue="--tables tss_count_tracking" falsevalue="" label="TSS count FPKM tracking" />
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33 <param type="boolean" name="tss_fpkm" truevalue="--tables tss_fpkm" falsevalue="" label="TSS groups FPKM tracking" />
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34 <param type="boolean" name="tss_rg" truevalue="--tables tss_rg" falsevalue="" label="TSS read groups" />
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35 <param type="boolean" name="var_model" truevalue="--tables var_model" falsevalue="" label="var_model.info" />
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36 </inputs>
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37 <outputs>
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38 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
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39 <filter>(cds_count is True)</filter>
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40 </data>
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41 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
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42 <filter>(cds_diff is True)</filter>
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43 </data>
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44 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
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45 <filter>(cds_exp_diff is True)</filter>
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46 </data>
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47 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
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48 <filter>(cds_fpkm is True)</filter>
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49 </data>
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50 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
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51 <filter>(cds_rg is True)</filter>
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52 </data>
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53 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
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54 <filter>(gene_exp_diff is True)</filter>
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55 </data>
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56 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
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57 <filter>(genes_count is True)</filter>
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58 </data>
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59 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
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60 <filter>(genes_fpkm is True)</filter>
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61 </data>
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62 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
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63 <filter>(gene_rg is True)</filter>
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64 </data>
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65 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
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66 <filter>(isoform_exp_diff is True)</filter>
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67 </data>
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68 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
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69 <filter>(isoform_count is True)</filter>
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70 </data>
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71 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
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72 <filter>(isoform_fpkm is True)</filter>
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73 </data>
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74 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
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75 <filter>(isoform_rg is True)</filter>
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76 </data>
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77 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
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78 <filter>(promoters_diff is True)</filter>
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79 </data>
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80 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
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81 <filter>(read_groups is True)</filter>
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82 </data>
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83 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
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84 <filter>(run_info is True)</filter>
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85 </data>
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86 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
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87 <filter>(splicing_diff is True)</filter>
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88 </data>
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89 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
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90 <filter>(tss_group_exp is True)</filter>
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91 </data>
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92 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
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93 <filter>(tss_count_tracking is True)</filter>
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94 </data>
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95 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
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96 <filter>(tss_fpkm is True)</filter>
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97 </data>
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98 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
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99 <filter>(tss_rg is True)</filter>
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100 </data>
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101 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
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102 <filter>(var_model is True)</filter>
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103 </data>
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104 </outputs>
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105 <citations>
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106 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
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107 </citations>
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108 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
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109 <tests>
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110 <test>
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111 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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112 <param name="cds_count" value="True" />
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113 <param name="cds_diff" value="True" />
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114 <param name="cds_exp_diff" value="True" />
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115 <param name="cds_fpkm" value="True" />
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116 <param name="cds_rg" value="True" />
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117 <param name="gene_exp_diff" value="True" />
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118 <param name="genes_count" value="True" />
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119 <param name="genes_fpkm" value="True" />
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120 <param name="gene_rg" value="True" />
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121 <param name="isoform_exp_diff" value="True" />
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122 <param name="isoform_count" value="True" />
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123 <param name="isoform_fpkm" value="True" />
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124 <param name="isoform_rg" value="True" />
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125 <param name="promoters_diff" value="True" />
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126 <param name="read_groups" value="True" />
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127 <param name="run_info" value="True" />
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128 <param name="splicing_diff" value="True" />
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129 <param name="tss_group_exp" value="True" />
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130 <param name="tss_count_tracking" value="True" />
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131 <param name="tss_fpkm" value="True" />
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132 <param name="tss_rg" value="True" />
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133 <param name="var_model" value="True" />
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134 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
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135 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
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136 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
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137 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
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138 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
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139 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
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140 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
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141 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
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142 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
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143 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
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144 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
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145 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
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146 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
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147 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
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148 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
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149 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
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150 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
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151 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
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152 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
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153 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
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154 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
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155 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
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156 </test>
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157 <test>
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158 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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159 <param name="cds_count" value="True" />
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160 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
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161 </test>
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162 <test>
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163 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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164 <param name="cds_diff" value="True" />
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165 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
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166 </test>
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167 <test>
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168 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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169 <param name="cds_exp_diff" value="True" />
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170 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
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171 </test>
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172 <test>
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173 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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174 <param name="cds_fpkm" value="True" />
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175 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
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176 </test>
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177 <test>
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178 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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179 <param name="cds_rg" value="True" />
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180 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
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181 </test>
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182 <test>
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183 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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184 <param name="gene_exp_diff" value="True" />
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185 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
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186 </test>
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187 <test>
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188 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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189 <param name="genes_count" value="True" />
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190 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
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191 </test>
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192 <test>
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193 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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194 <param name="genes_fpkm" value="True" />
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195 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
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196 </test>
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197 <test>
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198 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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199 <param name="gene_rg" value="True" />
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200 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
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201 </test>
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202 <test>
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203 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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204 <param name="isoform_exp_diff" value="True" />
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205 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
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206 </test>
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207 <test>
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208 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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209 <param name="isoform_count" value="True" />
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210 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
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211 </test>
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212 <test>
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213 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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214 <param name="isoform_fpkm" value="True" />
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215 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
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216 </test>
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217 <test>
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218 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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219 <param name="isoform_rg" value="True" />
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220 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
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221 </test>
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222 <test>
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223 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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224 <param name="promoters_diff" value="True" />
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225 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
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226 </test>
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227 <test>
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228 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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229 <param name="read_groups" value="True" />
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230 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
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231 </test>
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232 <test>
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233 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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234 <param name="run_info" value="True" />
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235 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
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236 </test>
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237 <test>
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238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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239 <param name="splicing_diff" value="True" />
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240 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
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241 </test>
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242 <test>
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243 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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244 <param name="tss_group_exp" value="True" />
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245 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
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246 </test>
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247 <test>
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248 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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249 <param name="tss_count_tracking" value="True" />
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250 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
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251 </test>
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252 <test>
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253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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254 <param name="tss_fpkm" value="True" />
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255 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
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256 </test>
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257 <test>
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258 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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259 <param name="tss_rg" value="True" />
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260 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
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261 </test>
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262 <test>
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263 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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264 <param name="var_model" value="True" />
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265 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
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266 </test>
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267 </tests>
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268 </tool>
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