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