annotate cummerbund_wrapper.xml @ 9:532a336a14c1 default tip

Need all_fasta.loc for cummerbund
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:39:39 -0500
parents 137aab1d9ac1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
1 <tool id="cummerbund" name="cummeRbund" version="0.0.7">
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
3
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
3 <!--
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
4 <requirements>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
6 </requirements>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
7 -->
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
8 <command interpreter="python">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
9 cummerbund_wrapper.py
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
10 --r-script ${script_file}
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
11 --html-report-from-directory "${output_html}" "${output_html.files_path}"
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
12 </command>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
13
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
14 <inputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
15 <conditional name="backend_database_source">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
16 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
17 <option value="history" selected="true">Use backend database from the history</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
18 <option value="cuffdiff_output">Build backend database using cuffdiff output</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
19 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
20 <when value="cuffdiff_output">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
21 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
22 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
23 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
24 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
25 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
26 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
27 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
28 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
29 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
30 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
31 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
32 <param name="rebuild" type="hidden" value="TRUE"/>
3
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
33 <conditional name="reference">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
34 <param name="include" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Include genome reference and Feature file"/>`
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
35 <when value="yes">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
36 <param name="gtf_file" type="data" format="gtf,gff3" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
37 <conditional name="genome">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
38 <param name="source" type="select" label="Reference sequence data">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
39 <option value="cached">Locally cached</option>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
40 <option value="history">History</option>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
41 </param>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
42 <when value="cached">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
43 <param name="ref_fasta" type="select" label="Select the reference genome that was used for cuffdiff">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
44 <options from_data_table="all_fasta">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
45 <filter type="sort_by" column="2" />
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
46 <validator type="no_options" message="No reference fasta files are available" />
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
47 </options>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
48 </param>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
49 </when>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
50 <when value="history">
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
51 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
52 </when>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
53 </conditional>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
54 </when>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
55 <when value="no"/>
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
56 </conditional>
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
57 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
58 <when value="history">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
59 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
60 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
61 </conditional>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
62 <repeat name="plots" title="Plots">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
63 <param name="width" type="text" value="1280" label="The width of the image"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
64 <param name="height" type="text" value="960" label="The height of the image"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
65 <conditional name="plot">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
66 <param name="type" type="select" label="Plot type">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
67 <option value="density" selected="true">Density</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
68 <option value="dispersion">Dispersion</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
69 <option value="fpkmSCV">Squared Coefficient of Variation</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
70 <option value="scatterMatrix">Scatter Matrix</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
71 <option value="boxplot">Boxplot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
72 <option value="scatter">Scatter</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
73 <option value="volcano">Volcano</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
74 <option value="heatmap">Heatmap</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
75 <option value="cluster">Cluster</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
76 <option value="expressionplot">Expression Plot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
77 <option value="expressionbarplot">Expression Bar Plot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
78 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
79 <option value="pca">Principal Component Analysis (PCA) Plot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
80 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
81 <option value="dendrogram">Dendrogram</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
82 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
83 <when value="density">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
84 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
85 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
86 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
87 <when value="mds">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
88 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
89 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
90 <when value="pca">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
91 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
92 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
93 <when value="maplot">
2
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
94 <param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
95 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
96 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
97 <param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
98 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
99 </param>
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
100 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
101 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
102 <when value="dendrogram">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
103 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
104 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
105 <when value="dispersion">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
106 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
107 <when value="fpkmSCV">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
108 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
109 <when value="scatterMatrix">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
110 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
111 <when value="boxplot">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
112 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
113 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
114 <when value="scatter">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
115 <param name="x" type="text" label="Sample name for x axis"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
116 <param name="y" type="text" label="Sample name for y axis"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
117 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
118 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
119 <conditional name="multiple_genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
120 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
121 <when value="T">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
122 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
123 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
124 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
125 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
126 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
127 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
128 <repeat name="genes" title="Genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
129 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
130 </repeat>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
131 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
132 <when value="F"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
133 </conditional>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
134 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
135 <when value="volcano">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
136 <param name="x" type="text" label="First sample name for comparison"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
137 <param name="y" type="text" label="Second sample name for comparison"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
138 <conditional name="multiple_genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
139 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
140 <when value="T">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
141 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
142 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
143 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
144 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
145 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
146 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
147 <repeat name="genes" title="Genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
148 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
149 </repeat>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
150 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
151 <when value="F"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
152 </conditional>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
153 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
154 <when value="heatmap">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
155 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
156 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
157 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
158 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
159 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
160 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
161 <repeat name="genes" title="Genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
162 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
163 </repeat>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
164 <param name="clustering" type="select" label="Cluster by">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
165 <option value="row">Row</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
166 <option value="column">Column</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
167 <option value="both" selected="true">Both</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
168 <option value="none">None</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
169 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
170 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
171 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
172 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
173 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
174 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
175 <when value="cluster">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
176 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
177 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
178 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
179 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
180 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
181 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
182 <repeat name="genes" title="Genes">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
183 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
184 </repeat>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
185 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
186 <param name="iter_max" type="text" value="100" label="Max iterations"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
187 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
188 <when value="expressionplot">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
189 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
190 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
191 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
192 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
193 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
194 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
195 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
196 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
197 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
198 values for each condition?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
199 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
200 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
201 <when value="expressionbarplot">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
202 <param name="features" type="select" label="Expression levels to plot?">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
203 <option value="gene" selected="true">Genes</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
204 <option value="isoforms">Isoforms</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
205 <option value="tss">TSS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
206 <option value="cds">CDS</option>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
207 </param>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
208 <param name="gene_id" type="text" label="Gene ID"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
209 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
210 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
211 </when>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
212 </conditional>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
213 </repeat>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
214 </inputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
215 <stdio>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
216 <exit_code range="1:" level="fatal" description="CummerBund Error" />
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
217 </stdio>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
218 <outputs>
2
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
219 <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
220 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
221 </data>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
222 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
223 </outputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
224
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
225 <requirements>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
226 <requirement type="binary">R</requirement>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
227 </requirements>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
228
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
229 <!-->
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
230 <tests>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
231 <test>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
232 <param name="" value=""/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
233 <output name="" file=""/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
234 </test>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
235 </tests>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
236 -->
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
237 <configfiles>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
238 <configfile name="script_file">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
239
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
240 ## Feature Selection ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
241 get_features &lt;- function(myGenes, f="gene") {
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
242 if (f == "isoforms")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
243 return(isoforms(myGenes))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
244 else if (f == "tss")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
245 return(TSS(myGenes))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
246 else if (f == "cds")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
247 return(CDS(myGenes))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
248 else
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
249 return(myGenes)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
250 }
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
251
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
252 ## Main Function ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
253
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
254 ## Load cummeRbund library
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
255 library("cummeRbund")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
256
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
257 ## Initialize cuff object
3
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
258 #if $backend_database_source.backend_database_selector == "cuffdiff_output":
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
259 ## Check if gtfFIle and genome are includes
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
260 #set $gtf_link = None
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
261 #if $backend_database_source.reference.include:
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
262 #set $gtf_link = '.'.join(['cuff',$backend_database_source.reference.gtf_file.extension])
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
263 system('ln -s $backend_database_source.reference.gtf_file $gtf_link')
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
264 #if $backend_database_source.reference.genome.source == 'cached':
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
265 #set $ref_file = $backend_database_source.reference.genome.ref_fasta
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
266 #else
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
267 #set $ref_file = $backend_database_source.reference.genome.ref_file
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
268 #end if
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
269 #end if
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
270 cuff &lt;- readCufflinks(dir = "",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
271 dbFile = "${output_database}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
272 geneFPKM = "${genes_fpkm_tracking}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
273 geneDiff = "${genes_exp}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
274 isoformFPKM = "${isoforms_fpkm_tracking}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
275 isoformDiff = "${isoforms_exp}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
276 TSSFPKM = "${tss_groups_fpkm_tracking}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
277 TSSDiff = "${tss_groups_exp}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
278 CDSFPKM = "${cds_fpkm_tracking}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
279 CDSExpDiff = "${cds_exp_diff}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
280 CDSDiff = "${cds_diff}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
281 promoterFile = "${promoters_diff}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
282 splicingFile = "${splicing_diff}",
3
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
283 #if $gtf_link:
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
284 gtfFile = "${gtf_link}",
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
285 genome = "${ref_file}",
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
286 #end if
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
287 rebuild = T)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
288 #else:
3
f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
289 cuff &lt;- readCufflinks(dir = "",
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
290 dbFile = "${backend_database_source.input_database}",
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
291 rebuild = F)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
292 #end if
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
293
2
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
294 ## Print out info
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
295 print(cuff)
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
296 sink("cuffdb_info.txt")
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
297 print(cuff)
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
298 print("SAMPLES:")
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
299 samples(cuff)
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
300 print("REPLICATES:")
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
301 replicates(cuff)
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
302 print("FEATURES:")
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
303 print(annotation(genes(cuff)))
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
304 cat(annotation(genes(cuff))[[1]],sep=",")
2
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
305 sink()
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
306
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
307 #for $i, $p in enumerate($plots, start=1):
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
308 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
309 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
310 tryCatch({
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
311 ## Density plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
312 #if $p.plot['type'] == "density":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
313 csDensity(genes(cuff),replicates=$p.plot.replicates)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
314
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
315 ## Dispersion plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
316 #elif $p.plot['type'] == "dispersion":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
317 dispersionPlot(genes(cuff))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
318
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
319 ## Squared Coefficient of Variation plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
320 #elif $p.plot['type'] == "fpkmSCV":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
321 fpkmSCVPlot(genes(cuff))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
322
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
323 ## Scatter Matrix ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
324 #elif $p.plot['type'] == "scatterMatrix":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
325 csScatterMatrix(genes(cuff))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
326
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
327 ## Boxplot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
328 #elif $p.plot['type'] == "boxplot":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
329 csBoxplot(genes(cuff))
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
330
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
331 ## Scatter ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
332 #elif $p.plot['type'] == "scatter":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
333 #if $p.plot.multiple_genes['multiple_genes_selector']:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
334 myGeneIds &lt;- c()
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
335 #for $g in $p.plot.multiple_genes['genes']:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
336 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
337 #end for
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
338 myGenes &lt;- getGenes(cuff, myGeneIds)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
339 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
340 #else
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
341 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
342 #end if
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
343
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
344 ## Volcano ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
345 #elif $p.plot['type'] == "volcano":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
346 #if $p.plot.multiple_genes['multiple_genes_selector']:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
347 myGeneIds &lt;- c()
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
348 #for $g in $p.plot.multiple_genes['genes']:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
349 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
350 #end for
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
351 myGenes &lt;- getGenes(cuff, myGeneIds)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
352 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
353 #else
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
354 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
355 #end if
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
356
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
357 ## Heatmap ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
358 #elif $p.plot['type'] == "heatmap":
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
359 #if $p.plot.genes and len($p.plot.genes) > 0:
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
360 myGeneIds &lt;- c()
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
361 #for $g in $p.plot.genes:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
362 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
363 #end for
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
364 myGenes &lt;- getGenes(cuff, myGeneIds)
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
365 #else
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
366 myGenes &lt;- getGenes(cuff,annotation(genes(cuff))[[1]])
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
367 #end if
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
368 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
369
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
370 ## Cluster ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
371 #elif $p.plot['type'] == "cluster":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
372 myGeneIds &lt;- c()
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
373 #for $g in $p.plot.genes:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
374 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
375 #end for
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
376 myGenes &lt;- getGenes(cuff, myGeneIds)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
377 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
378
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
379 ## Expression Plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
380 #elif $p.plot['type'] == "expressionplot":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
381 myGeneId &lt;- "$p.plot.gene_id"
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
382 myGenes &lt;- getGenes(cuff, myGeneId)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
383 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
384
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
385 ## Expression Bar Plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
386 #elif $p.plot['type'] == "expressionbarplot":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
387 myGeneId &lt;- "$p.plot.gene_id"
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
388 myGenes &lt;- getGenes(cuff, myGeneId)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
389 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
390
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
391 ## MDS plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
392 #elif $p.plot['type'] == "mds":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
393 MDSplot(genes(cuff),replicates=$p.plot.replicates)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
394
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
395 ## PCA plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
396 #elif $p.plot['type'] == "pca":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
397 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
398
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
399 ## MAplot plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
400 #elif $p.plot['type'] == "maplot":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
401 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count})
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
402
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
403 ## Dendogram plot ##
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
404 #elif $p.plot['type'] == "dendrogram":
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
405 csDendro(genes(cuff),replicates=$p.plot.replicates)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
406 #end if
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
407
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
408 },error = function(e) {paste("$p.plot['type'] failed: ", e)})
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
409 devname = dev.off()
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
410
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
411 #end for
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
412 </configfile>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
413 </configfiles>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
414
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
415 <help>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
416 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
417 </help>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
418
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
419 </tool>