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1 <?xml version="1.0"?>
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2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1">
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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} ${' '.join(str($tables).split(','))}
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6 ]]></command>
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7 <inputs>
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8 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
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9 <param type="select" name="tables" multiple="True" label="Select tables to output">
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10 <option name="cds_count" value="--tables cds_count">CDS count tracking</option>
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11 <option name="cds_diff" value="--tables cds_diff">CDS overloading diffential expression testing</option>
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12 <option name="cds_exp_diff" value="--tables cds_exp_diff">CDS FPKM differential expression testing</option>
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13 <option name="cds_fpkm" value="--tables cds_fpkm">CDS FPKM tracking</option>
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14 <option name="cds_rg" value="--tables cds_rg">CDS read groups</option>
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15 <option name="gene_exp_diff" value="--tables gene_exp_diff">Gene differential expression testing</option>
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16 <option name="genes_count" value="--tables genes_count">Gene count tracking</option>
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17 <option name="genes_fpkm" value="--tables genes_fpkm">Gene FPKM tracking</option>
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18 <option name="gene_rg" value="--tables gene_rg">Gene read groups</option>
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19 <option name="isoform_exp_diff" value="--tables isoform_exp_diff">Transcript differential expression testing</option>
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20 <option name="isoform_count" value="--tables isoform_count">Transcript count tracking</option>
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21 <option name="isoform_fpkm" value="--tables isoform_fpkm">Transcript FPKM tracking</option>
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22 <option name="isoform_rg" value="--tables isoform_rg">Transcript read groups</option>
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23 <option name="promoters_diff" value="--tables promoters_diff">Promoter differential testing</option>
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24 <option name="read_groups" value="--tables read_groups">Read Groups</option>
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25 <option name="run_info" value="--tables run_info">Run details</option>
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26 <option name="splicing_diff" value="--tables splicing_diff">Splicing differential expression testing</option>
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27 <option name="tss_group_exp" value="--tables tss_group_exp">TSS groups differential expression testing</option>
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28 <option name="tss_count_tracking" value="--tables tss_count_tracking">TSS count FPKM tracking</option>
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29 <option name="tss_fpkm" value="--tables tss_fpkm">TSS groups FPKM tracking</option>
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30 <option name="tss_rg" value="--tables tss_rg">TSS read groups</option>
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31 <option name="var_model" value="--tables var_model">Model info</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
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36 <filter>('--tables cds_count' in tables)</filter>
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37 </data>
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38 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
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39 <filter>('--tables cds_diff' in tables)</filter>
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40 </data>
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41 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
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42 <filter>('--tables cds_exp_diff' in tables)</filter>
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43 </data>
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44 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
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45 <filter>('--tables cds_fpkm' in tables)</filter>
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46 </data>
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47 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
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48 <filter>('--tables cds_rg' in tables)</filter>
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49 </data>
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50 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
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51 <filter>('--tables gene_exp_diff' in tables)</filter>
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52 </data>
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53 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
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54 <filter>('--tables genes_count' in tables)</filter>
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55 </data>
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56 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
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57 <filter>('--tables genes_fpkm' in tables)</filter>
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58 </data>
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59 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
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60 <filter>('--tables gene_rg' in tables)</filter>
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61 </data>
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62 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
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63 <filter>('--tables isoform_exp_diff' in tables)</filter>
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64 </data>
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65 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
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66 <filter>('--tables isoform_count' in tables)</filter>
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67 </data>
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68 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
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69 <filter>('--tables isoform_fpkm' in tables)</filter>
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70 </data>
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71 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
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72 <filter>('--tables isoform_rg' in tables)</filter>
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73 </data>
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74 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
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75 <filter>('--tables promoters_diff' in tables)</filter>
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76 </data>
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77 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
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78 <filter>('--tables read_groups' in tables)</filter>
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79 </data>
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80 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
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81 <filter>('--tables run_info' in tables)</filter>
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82 </data>
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83 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
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84 <filter>('--tables splicing_diff' in tables)</filter>
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85 </data>
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86 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
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87 <filter>('--tables tss_group_exp' in tables)</filter>
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88 </data>
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89 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
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90 <filter>('--tables tss_count_tracking' in tables)</filter>
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91 </data>
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92 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
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93 <filter>('--tables tss_fpkm' in tables)</filter>
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94 </data>
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95 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
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96 <filter>('--tables tss_rg' in tables)</filter>
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97 </data>
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98 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
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99 <filter>('--tables var_model' in tables)</filter>
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100 </data>
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101 </outputs>
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102 <citations>
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103 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
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104 </citations>
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105 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
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106 <tests>
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107 <test>
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108 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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109 <param name="tables" value="--tables cds_count,--tables cds_diff,--tables cds_exp_diff,--tables cds_fpkm,--tables cds_rg,--tables gene_exp_diff,--tables genes_count,--tables genes_fpkm,--tables gene_rg,--tables isoform_exp_diff,--tables isoform_count,--tables isoform_fpkm,--tables isoform_rg,--tables promoters_diff,--tables read_groups,--tables run_info,--tables splicing_diff,--tables tss_group_exp,--tables tss_count_tracking,--tables tss_fpkm,--tables tss_rg,--tables var_model" />
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110 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
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111 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
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112 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
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113 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
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114 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
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115 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
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116 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
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117 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
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118 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
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119 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
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120 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
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121 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
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122 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
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123 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
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124 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
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125 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
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126 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
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127 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
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128 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
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129 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
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130 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
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131 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
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132 </test>
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133 <test>
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134 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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135 <param name="tables" value="--tables cds_count" />
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136 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
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137 </test>
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138 <test>
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139 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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140 <param name="tables" value="--tables cds_diff" />
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141 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
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142 </test>
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143 <test>
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144 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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145 <param name="tables" value="--tables cds_exp_diff" />
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146 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
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147 </test>
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148 <test>
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149 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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150 <param name="tables" value="--tables cds_fpkm" />
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151 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
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152 </test>
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153 <test>
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154 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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155 <param name="tables" value="--tables cds_rg" />
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156 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
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157 </test>
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158 <test>
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159 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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160 <param name="tables" value="--tables gene_exp_diff" />
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161 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
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162 </test>
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163 <test>
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164 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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165 <param name="tables" value="--tables genes_count" />
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166 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
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167 </test>
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168 <test>
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169 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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170 <param name="tables" value="--tables genes_fpkm" />
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171 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
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172 </test>
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173 <test>
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174 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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175 <param name="tables" value="--tables gene_rg" />
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176 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
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177 </test>
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178 <test>
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179 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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180 <param name="tables" value="--tables isoform_exp_diff" />
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181 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
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182 </test>
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183 <test>
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184 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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185 <param name="tables" value="--tables isoform_count" />
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186 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
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187 </test>
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188 <test>
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189 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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190 <param name="tables" value="--tables isoform_fpkm" />
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191 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
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192 </test>
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193 <test>
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194 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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195 <param name="tables" value="--tables isoform_rg" />
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196 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
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197 </test>
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198 <test>
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199 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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200 <param name="tables" value="--tables promoters_diff" />
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201 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
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202 </test>
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203 <test>
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204 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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205 <param name="tables" value="--tables read_groups" />
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206 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
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207 </test>
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208 <test>
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209 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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210 <param name="tables" value="--tables run_info" />
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211 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
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212 </test>
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213 <test>
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214 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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215 <param name="tables" value="--tables splicing_diff" />
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216 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
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217 </test>
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218 <test>
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219 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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220 <param name="tables" value="--tables tss_group_exp" />
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221 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
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222 </test>
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223 <test>
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224 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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225 <param name="tables" value="--tables tss_count_tracking" />
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226 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
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227 </test>
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228 <test>
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229 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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230 <param name="tables" value="--tables tss_fpkm" />
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231 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
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232 </test>
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233 <test>
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234 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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235 <param name="tables" value="--tables tss_rg" />
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236 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
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237 </test>
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238 <test>
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239 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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240 <param name="tables" value="--tables var_model" />
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241 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
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242 </test>
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243 </tests>
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244 </tool>
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