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comparison cuffdata_datasets.xml @ 0:da7241f92ecf

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author jjohnson
date Mon, 04 Feb 2013 19:50:25 -0500
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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>