|
0
|
1 <?xml version="1.0"?>
|
|
1
|
2 <tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1">
|
|
0
|
3 <description>tabular files from a cummeRbund database</description>
|
|
|
4 <command interpreter="python"><![CDATA[
|
|
|
5 cummerbund_to_tabular.py --file ${input_database}
|
|
|
6 ${cds_count} ${cds_diff} ${cds_exp_diff} ${cds_fpkm} ${cds_rg}
|
|
|
7 ${gene_exp_diff} ${genes_count} ${genes_fpkm} ${gene_rg} ${isoform_exp_diff}
|
|
|
8 ${isoform_count} ${isoform_fpkm} ${isoform_rg} ${promoters_diff} ${read_groups}
|
|
|
9 ${run_info} ${splicing_diff} ${tss_group_exp} ${tss_count_tracking} ${tss_fpkm}
|
|
|
10 ${tss_rg} ${var_model}
|
|
|
11 ]]></command>
|
|
|
12 <inputs>
|
|
|
13 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
|
|
|
14 <param type="boolean" name="cds_count" truevalue="--tables cds_count" falsevalue="" label="CDS count tracking" />
|
|
|
15 <param type="boolean" name="cds_diff" truevalue="--tables cds_diff" falsevalue="" label="CDS overloading diffential expression testing" />
|
|
|
16 <param type="boolean" name="cds_exp_diff" truevalue="--tables cds_exp_diff" falsevalue="" label="CDS FPKM differential expression testing" />
|
|
|
17 <param type="boolean" name="cds_fpkm" truevalue="--tables cds_fpkm" falsevalue="" label="CDS FPKM tracking" />
|
|
|
18 <param type="boolean" name="cds_rg" truevalue="--tables cds_rg" falsevalue="" label="CDS read groups" />
|
|
|
19 <param type="boolean" name="gene_exp_diff" truevalue="--tables gene_exp_diff" falsevalue="" label="gene differential expression testing" />
|
|
|
20 <param type="boolean" name="genes_count" truevalue="--tables genes_count" falsevalue="" label="gene count tracking" />
|
|
|
21 <param type="boolean" name="genes_fpkm" truevalue="--tables genes_fpkm" falsevalue="" label="gene FPKM tracking" />
|
|
|
22 <param type="boolean" name="gene_rg" truevalue="--tables gene_rg" falsevalue="" label="gene read groups" />
|
|
|
23 <param type="boolean" name="isoform_exp_diff" truevalue="--tables isoform_exp_diff" falsevalue="" label="transcript differential expression testing" />
|
|
|
24 <param type="boolean" name="isoform_count" truevalue="--tables isoform_count" falsevalue="" label="transcript count tracking" />
|
|
|
25 <param type="boolean" name="isoform_fpkm" truevalue="--tables isoform_fpkm" falsevalue="" label="transcript FPKM tracking" />
|
|
|
26 <param type="boolean" name="isoform_rg" truevalue="--tables isoform_rg" falsevalue="" label="transcript read groups" />
|
|
|
27 <param type="boolean" name="promoters_diff" truevalue="--tables promoters_diff" falsevalue="" label="promoter differential testing" />
|
|
|
28 <param type="boolean" name="read_groups" truevalue="--tables read_groups" falsevalue="" label="Read Groups" />
|
|
|
29 <param type="boolean" name="run_info" truevalue="--tables run_info" falsevalue="" label="Run details" />
|
|
|
30 <param type="boolean" name="splicing_diff" truevalue="--tables splicing_diff" falsevalue="" label="splicing differential expression testing" />
|
|
|
31 <param type="boolean" name="tss_group_exp" truevalue="--tables tss_group_exp" falsevalue="" label="TSS groups differential expression testing" />
|
|
|
32 <param type="boolean" name="tss_count_tracking" truevalue="--tables tss_count_tracking" falsevalue="" label="TSS count FPKM tracking" />
|
|
|
33 <param type="boolean" name="tss_fpkm" truevalue="--tables tss_fpkm" falsevalue="" label="TSS groups FPKM tracking" />
|
|
|
34 <param type="boolean" name="tss_rg" truevalue="--tables tss_rg" falsevalue="" label="TSS read groups" />
|
|
|
35 <param type="boolean" name="var_model" truevalue="--tables var_model" falsevalue="" label="var_model.info" />
|
|
|
36 </inputs>
|
|
|
37 <outputs>
|
|
|
38 <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
|
|
|
39 <filter>(cds_count is True)</filter>
|
|
|
40 </data>
|
|
|
41 <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
|
|
|
42 <filter>(cds_diff is True)</filter>
|
|
|
43 </data>
|
|
|
44 <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
|
|
|
45 <filter>(cds_exp_diff is True)</filter>
|
|
|
46 </data>
|
|
|
47 <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
|
|
|
48 <filter>(cds_fpkm is True)</filter>
|
|
|
49 </data>
|
|
|
50 <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
|
|
|
51 <filter>(cds_rg is True)</filter>
|
|
|
52 </data>
|
|
|
53 <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
|
|
|
54 <filter>(gene_exp_diff is True)</filter>
|
|
|
55 </data>
|
|
|
56 <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
|
|
|
57 <filter>(genes_count is True)</filter>
|
|
|
58 </data>
|
|
|
59 <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
|
|
|
60 <filter>(genes_fpkm is True)</filter>
|
|
|
61 </data>
|
|
|
62 <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
|
|
|
63 <filter>(gene_rg is True)</filter>
|
|
|
64 </data>
|
|
|
65 <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
|
|
|
66 <filter>(isoform_exp_diff is True)</filter>
|
|
|
67 </data>
|
|
|
68 <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
|
|
|
69 <filter>(isoform_count is True)</filter>
|
|
|
70 </data>
|
|
|
71 <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
|
|
|
72 <filter>(isoform_fpkm is True)</filter>
|
|
|
73 </data>
|
|
|
74 <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
|
|
|
75 <filter>(isoform_rg is True)</filter>
|
|
|
76 </data>
|
|
|
77 <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
|
|
|
78 <filter>(promoters_diff is True)</filter>
|
|
|
79 </data>
|
|
|
80 <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
|
|
|
81 <filter>(read_groups is True)</filter>
|
|
|
82 </data>
|
|
|
83 <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
|
|
|
84 <filter>(run_info is True)</filter>
|
|
|
85 </data>
|
|
|
86 <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
|
|
|
87 <filter>(splicing_diff is True)</filter>
|
|
|
88 </data>
|
|
|
89 <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
|
|
|
90 <filter>(tss_group_exp is True)</filter>
|
|
|
91 </data>
|
|
|
92 <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
|
|
|
93 <filter>(tss_count_tracking is True)</filter>
|
|
|
94 </data>
|
|
|
95 <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
|
|
|
96 <filter>(tss_fpkm is True)</filter>
|
|
|
97 </data>
|
|
|
98 <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
|
|
|
99 <filter>(tss_rg is True)</filter>
|
|
|
100 </data>
|
|
|
101 <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
|
|
|
102 <filter>(var_model is True)</filter>
|
|
|
103 </data>
|
|
|
104 </outputs>
|
|
|
105 <citations>
|
|
|
106 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
|
|
|
107 </citations>
|
|
|
108 <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
|
|
|
109 <tests>
|
|
|
110 <test>
|
|
|
111 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
112 <param name="cds_count" value="True" />
|
|
|
113 <param name="cds_diff" value="True" />
|
|
|
114 <param name="cds_exp_diff" value="True" />
|
|
|
115 <param name="cds_fpkm" value="True" />
|
|
|
116 <param name="cds_rg" value="True" />
|
|
|
117 <param name="gene_exp_diff" value="True" />
|
|
|
118 <param name="genes_count" value="True" />
|
|
|
119 <param name="genes_fpkm" value="True" />
|
|
|
120 <param name="gene_rg" value="True" />
|
|
|
121 <param name="isoform_exp_diff" value="True" />
|
|
|
122 <param name="isoform_count" value="True" />
|
|
|
123 <param name="isoform_fpkm" value="True" />
|
|
|
124 <param name="isoform_rg" value="True" />
|
|
|
125 <param name="promoters_diff" value="True" />
|
|
|
126 <param name="read_groups" value="True" />
|
|
|
127 <param name="run_info" value="True" />
|
|
|
128 <param name="splicing_diff" value="True" />
|
|
|
129 <param name="tss_group_exp" value="True" />
|
|
|
130 <param name="tss_count_tracking" value="True" />
|
|
|
131 <param name="tss_fpkm" value="True" />
|
|
|
132 <param name="tss_rg" value="True" />
|
|
|
133 <param name="var_model" value="True" />
|
|
|
134 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
|
|
|
135 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
|
|
|
136 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
|
|
|
137 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
|
|
|
138 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
|
|
|
139 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
|
|
|
140 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
|
|
|
141 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
|
|
|
142 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
|
|
|
143 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
|
|
|
144 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
|
|
|
145 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
|
|
|
146 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
|
|
|
147 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
|
|
|
148 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
|
|
|
149 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
|
|
|
150 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
|
|
|
151 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
|
|
|
152 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
|
|
|
153 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
|
|
|
154 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
|
|
|
155 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
|
|
|
156 </test>
|
|
|
157 <test>
|
|
|
158 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
159 <param name="cds_count" value="True" />
|
|
|
160 <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
|
|
|
161 </test>
|
|
|
162 <test>
|
|
|
163 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
164 <param name="cds_diff" value="True" />
|
|
|
165 <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
|
|
|
166 </test>
|
|
|
167 <test>
|
|
|
168 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
169 <param name="cds_exp_diff" value="True" />
|
|
|
170 <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
|
|
|
171 </test>
|
|
|
172 <test>
|
|
|
173 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
174 <param name="cds_fpkm" value="True" />
|
|
|
175 <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
|
|
|
176 </test>
|
|
|
177 <test>
|
|
|
178 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
179 <param name="cds_rg" value="True" />
|
|
|
180 <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
|
|
|
181 </test>
|
|
|
182 <test>
|
|
|
183 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
184 <param name="gene_exp_diff" value="True" />
|
|
|
185 <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
|
|
|
186 </test>
|
|
|
187 <test>
|
|
|
188 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
189 <param name="genes_count" value="True" />
|
|
|
190 <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
|
|
|
191 </test>
|
|
|
192 <test>
|
|
|
193 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
194 <param name="genes_fpkm" value="True" />
|
|
|
195 <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
|
|
|
196 </test>
|
|
|
197 <test>
|
|
|
198 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
199 <param name="gene_rg" value="True" />
|
|
|
200 <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
|
|
|
201 </test>
|
|
|
202 <test>
|
|
|
203 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
204 <param name="isoform_exp_diff" value="True" />
|
|
|
205 <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
|
|
|
206 </test>
|
|
|
207 <test>
|
|
|
208 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
209 <param name="isoform_count" value="True" />
|
|
|
210 <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
|
|
|
211 </test>
|
|
|
212 <test>
|
|
|
213 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
214 <param name="isoform_fpkm" value="True" />
|
|
|
215 <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
|
|
|
216 </test>
|
|
|
217 <test>
|
|
|
218 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
219 <param name="isoform_rg" value="True" />
|
|
|
220 <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
|
|
|
221 </test>
|
|
|
222 <test>
|
|
|
223 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
224 <param name="promoters_diff" value="True" />
|
|
|
225 <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
|
|
|
226 </test>
|
|
|
227 <test>
|
|
|
228 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
229 <param name="read_groups" value="True" />
|
|
|
230 <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
|
|
|
231 </test>
|
|
|
232 <test>
|
|
|
233 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
234 <param name="run_info" value="True" />
|
|
|
235 <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
|
|
|
236 </test>
|
|
|
237 <test>
|
|
|
238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
239 <param name="splicing_diff" value="True" />
|
|
|
240 <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
|
|
|
241 </test>
|
|
|
242 <test>
|
|
|
243 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
244 <param name="tss_group_exp" value="True" />
|
|
|
245 <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
|
|
|
246 </test>
|
|
|
247 <test>
|
|
|
248 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
249 <param name="tss_count_tracking" value="True" />
|
|
|
250 <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
|
|
|
251 </test>
|
|
|
252 <test>
|
|
|
253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
254 <param name="tss_fpkm" value="True" />
|
|
|
255 <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
|
|
|
256 </test>
|
|
|
257 <test>
|
|
|
258 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
259 <param name="tss_rg" value="True" />
|
|
|
260 <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
|
|
|
261 </test>
|
|
|
262 <test>
|
|
|
263 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
|
|
|
264 <param name="var_model" value="True" />
|
|
|
265 <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
|
|
|
266 </test>
|
|
|
267 </tests>
|
|
|
268 </tool>
|
