|
0
|
1 <tool id="cuffdata_datasets" name="Cuffdata datasets" version="0.0.6">
|
|
|
2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
|
|
|
3 <description>history datasets from Cuffdiff output</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package">cufflinks</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 #set sel_outputs = $output_sel.__str__.split(',')
|
|
|
9 #if 'run_info' in $sel_outputs:
|
|
|
10 cat ${cuffdata.extra_files_path}/run.info > $run_info;
|
|
|
11 #end if
|
|
|
12 #if 'read_groups_info' in $sel_outputs:
|
|
|
13 cat ${cuffdata.extra_files_path}/read_groups.info > $read_groups_info;
|
|
|
14 #end if
|
|
|
15
|
|
|
16 #if 'splicing_diff' in $sel_outputs:
|
|
|
17 cat ${cuffdata.extra_files_path}/splicing.diff > $splicing_diff;
|
|
|
18 #end if
|
|
|
19 #if 'promoters_diff' in $sel_outputs:
|
|
|
20 cat ${cuffdata.extra_files_path}/promoters.diff > $promoters_diff;
|
|
|
21 #end if
|
|
|
22
|
|
|
23 #if 'cds_diff' in $sel_outputs:
|
|
|
24 cat ${cuffdata.extra_files_path}/cds.diff > $cds_diff;
|
|
|
25 #end if
|
|
|
26 #if 'cds_exp_diff' in $sel_outputs:
|
|
|
27 cat ${cuffdata.extra_files_path}/cds_exp.diff > $cds_exp_diff;
|
|
|
28 #end if
|
|
|
29 #if 'cds_fpkm_tracking' in $sel_outputs:
|
|
|
30 cat ${cuffdata.extra_files_path}/cds.fpkm_tracking > $cds_fpkm_tracking;
|
|
|
31 #end if
|
|
|
32 #if 'cds_count_tracking' in $sel_outputs:
|
|
|
33 cat ${cuffdata.extra_files_path}/cds.count_tracking > $cds_count_tracking;
|
|
|
34 #end if
|
|
|
35 #if 'cds_read_group_tracking' in $sel_outputs:
|
|
|
36 cat ${cuffdata.extra_files_path}/cds.read_group_tracking > $cds_read_group_tracking;
|
|
|
37 #end if
|
|
|
38
|
|
|
39 #if 'tss_groups_exp_diff' in $sel_outputs:
|
|
|
40 cat ${cuffdata.extra_files_path}/tss_groups_exp.diff > $tss_groups_exp_diff;
|
|
|
41 #end if
|
|
|
42 #if 'tss_groups_fpkm_tracking' in $sel_outputs:
|
|
|
43 cat ${cuffdata.extra_files_path}/tss_groups.fpkm_tracking > $tss_groups_fpkm_tracking;
|
|
|
44 #end if
|
|
|
45 #if 'tss_groups_count_tracking' in $sel_outputs:
|
|
|
46 cat ${cuffdata.extra_files_path}/tss_groups.count_tracking > $tss_groups_count_tracking;
|
|
|
47 #end if
|
|
|
48 #if 'tss_groups_read_group_tracking' in $sel_outputs:
|
|
|
49 cat ${cuffdata.extra_files_path}/tss_groups.read_group_tracking > $tss_groups_read_group_tracking;
|
|
|
50 #end if
|
|
|
51
|
|
|
52 #if 'genes_exp_diff' in $sel_outputs:
|
|
|
53 cat ${cuffdata.extra_files_path}/genes_exp.diff > $genes_exp_diff;
|
|
|
54 #end if
|
|
|
55 #if 'genes_fpkm_tracking' in $sel_outputs:
|
|
|
56 cat ${cuffdata.extra_files_path}/genes.fpkm_tracking > $genes_fpkm_tracking;
|
|
|
57 #end if
|
|
|
58 #if 'genes_count_tracking' in $sel_outputs:
|
|
|
59 cat ${cuffdata.extra_files_path}/genes.count_tracking > $genes_count_tracking;
|
|
|
60 #end if
|
|
|
61 #if 'genes_read_group_tracking' in $sel_outputs:
|
|
|
62 cat ${cuffdata.extra_files_path}/genes.read_group_tracking > $genes_read_group_tracking;
|
|
|
63 #end if
|
|
|
64
|
|
|
65 #if 'isoforms_exp_diff' in $sel_outputs:
|
|
|
66 cat ${cuffdata.extra_files_path}/isoforms_exp.diff > $isoforms_exp_diff;
|
|
|
67 #end if
|
|
|
68 #if 'isoforms_fpkm_tracking' in $sel_outputs:
|
|
|
69 cat ${cuffdata.extra_files_path}/isoforms.fpkm_tracking > $isoforms_fpkm_tracking;
|
|
|
70 #end if
|
|
|
71 #if 'isoforms_count_tracking' in $sel_outputs:
|
|
|
72 cat ${cuffdata.extra_files_path}/isoforms.count_tracking > $isoforms_count_tracking;
|
|
|
73 #end if
|
|
|
74 #if 'isoforms_read_group_tracking' in $sel_outputs:
|
|
|
75 cat ${cuffdata.extra_files_path}/isoforms.read_group_tracking > $isoforms_read_group_tracking;
|
|
|
76 #end if
|
|
|
77
|
|
|
78 </command>
|
|
|
79 <inputs>
|
|
|
80 <param name="cuffdata" type="data" format="cuffdata" label="Cuffidif cuffdata" help=""/>
|
|
|
81 <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
|
|
|
82 <option value="run_info">run.info</option>
|
|
|
83 <option value="read_groups_info">read_groups.info</option>
|
|
|
84 <option value="splicing_diff">splicing.diff</option>
|
|
|
85 <option value="promoters_diff">promoters.diff</option>
|
|
|
86 <option value="genes_exp_diff">genes_exp.diff</option>
|
|
|
87 <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
|
|
|
88 <option value="genes_count_tracking">genes.count_tracking</option>
|
|
|
89 <option value="genes_read_group_tracking">genes.read_group_tracking</option>
|
|
|
90 <option value="isoforms_exp_diff">isoforms.exp_diff</option>
|
|
|
91 <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
|
|
|
92 <option value="isoforms_count_tracking">isoforms.count_tracking</option>
|
|
|
93 <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
|
|
|
94 <option value="cds_diff">cds.diff</option>
|
|
|
95 <option value="cds_exp_diff">cds_exp.diff</option>
|
|
|
96 <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
|
|
|
97 <option value="cds_count_tracking">cds.count_tracking</option>
|
|
|
98 <option value="cds_read_group_tracking">cds.read_group_tracking</option>
|
|
|
99 <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
|
|
|
100 <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
|
|
|
101 <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
|
|
|
102 <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
|
|
|
103 </param>
|
|
|
104 </inputs>
|
|
|
105
|
|
|
106 <outputs>
|
|
|
107 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
|
|
|
108 <filter>'run_info' in output_sel</filter>
|
|
|
109 </data>
|
|
|
110 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
|
|
|
111 <filter>'read_groups_info' in output_sel</filter>
|
|
|
112 </data>
|
|
|
113 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
|
|
|
114 <filter>'splicing_diff' in output_sel</filter>
|
|
|
115 </data>
|
|
|
116 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
|
|
|
117 <filter>'promoters_diff' in output_sel</filter>
|
|
|
118 </data>
|
|
|
119 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
|
|
|
120 <filter>'cds_diff' in output_sel</filter>
|
|
|
121 </data>
|
|
|
122 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
|
|
|
123 <filter>'cds_exp_diff' in output_sel</filter>
|
|
|
124 </data>
|
|
|
125 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
|
|
|
126 <filter>'cds_fpkm_tracking' in output_sel</filter>
|
|
|
127 </data>
|
|
|
128 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
|
|
|
129 <filter>'cds_count_tracking' in output_sel</filter>
|
|
|
130 </data>
|
|
|
131 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
|
|
|
132 <filter>'cds_read_group_tracking' in output_sel</filter>
|
|
|
133 </data>
|
|
|
134 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
|
|
|
135 <filter>'tss_groups_exp_diff' in output_sel</filter>
|
|
|
136 </data>
|
|
|
137 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
|
|
|
138 <filter>'tss_groups_fpkm_tracking' in output_sel</filter>
|
|
|
139 </data>
|
|
|
140 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
|
|
|
141 <filter>'tss_groups_count_tracking' in output_sel</filter>
|
|
|
142 </data>
|
|
|
143 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
|
|
|
144 <filter>'tss_groups_read_group_tracking' in output_sel</filter>
|
|
|
145 </data>
|
|
|
146 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
|
|
|
147 <filter>'isoforms_exp_diff' in output_sel</filter>
|
|
|
148 </data>
|
|
|
149 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
|
|
|
150 <filter>'isoforms_fpkm_tracking' in output_sel</filter>
|
|
|
151 </data>
|
|
|
152 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
|
|
|
153 <filter>'isoforms_count_tracking' in output_sel</filter>
|
|
|
154 </data>
|
|
|
155 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
|
|
|
156 <filter>'isoforms_read_group_tracking' in output_sel</filter>
|
|
|
157 </data>
|
|
|
158 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
|
|
|
159 <filter>'genes_exp_diff' in output_sel</filter>
|
|
|
160 </data>
|
|
|
161 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
|
|
|
162 <filter>'genes_fpkm_tracking' in output_sel</filter>
|
|
|
163 </data>
|
|
|
164 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
|
|
|
165 <filter>'genes_count_tracking' in output_sel</filter>
|
|
|
166 </data>
|
|
|
167 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
|
|
|
168 <filter>'genes_read_group_tracking' in output_sel</filter>
|
|
|
169 </data>
|
|
|
170 </outputs>
|
|
|
171 <stdio>
|
|
|
172 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
|
|
|
173 </stdio>
|
|
|
174
|
|
|
175
|
|
|
176 <tests>
|
|
|
177 </tests>
|
|
|
178
|
|
|
179 <help>
|
|
|
180 **Cuffdata to history datasets**
|
|
|
181
|
|
|
182 Copy Cuffdiff output files from a cuffdata html page to datasets in your history.
|
|
|
183
|
|
|
184 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
|
|
|
185
|
|
|
186 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
|
|
|
187
|
|
|
188 </help>
|
|
|
189 </tool>
|
