Mercurial > repos > jjohnson > cummerbund
annotate cummerbund_wrapper.xml @ 3:f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 15 Nov 2013 13:39:14 -0600 |
| parents | fdf01b3c1841 |
| children | 137aab1d9ac1 |
| rev | line source |
|---|---|
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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
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1 <tool id="cummerbund" name="cummeRbund" version="0.0.7"> |
| 0 | 2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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3 <!-- |
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f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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4 <requirements> |
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f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement> |
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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:
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6 </requirements> |
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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:
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changeset
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7 --> |
| 0 | 8 <command interpreter="python"> |
| 9 cummerbund_wrapper.py | |
| 10 --r-script ${script_file} | |
| 11 --html-report-from-directory "${output_html}" "${output_html.files_path}" | |
| 12 </command> | |
| 13 | |
| 14 <inputs> | |
| 15 <conditional name="backend_database_source"> | |
| 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?"> | |
| 17 <option value="history" selected="true">Use backend database from the history</option> | |
| 18 <option value="cuffdiff_output">Build backend database using cuffdiff output</option> | |
| 19 </param> | |
| 20 <when value="cuffdiff_output"> | |
| 21 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/> | |
| 22 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/> | |
| 23 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/> | |
| 24 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/> | |
| 25 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/> | |
| 26 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/> | |
| 27 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/> | |
| 28 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/> | |
| 29 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/> | |
| 30 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/> | |
| 31 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/> | |
| 32 <param name="rebuild" type="hidden" value="TRUE"/> | |
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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:
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33 <conditional name="reference"> |
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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:
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34 <param name="include" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Include genome reference and Feature file"/>` |
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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
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changeset
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35 <when value="yes"> |
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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:
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changeset
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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."/> |
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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
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changeset
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37 <conditional name="genome"> |
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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
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38 <param name="source" type="select" label="Reference sequence data"> |
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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:
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39 <option value="cached">Locally cached</option> |
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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
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40 <option value="history">History</option> |
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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
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41 </param> |
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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
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42 <when value="cached"> |
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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
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43 <param name="ref_fasta" type="select" label="Select the reference genome that was used for cuffdiff"> |
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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
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44 <options from_data_table="all_fasta"> |
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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
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45 <filter type="sort_by" column="2" /> |
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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
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46 <validator type="no_options" message="No reference fasta files are available" /> |
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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
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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
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48 </param> |
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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
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49 </when> |
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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" /> |
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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
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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> |
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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
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55 <when value="no"/> |
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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 | 57 </when> |
| 58 <when value="history"> | |
| 59 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/> | |
| 60 </when> | |
| 61 </conditional> | |
| 62 <repeat name="plots" title="Plots"> | |
| 63 <param name="width" type="text" value="1280" label="The width of the image"/> | |
| 64 <param name="height" type="text" value="960" label="The height of the image"/> | |
| 65 <conditional name="plot"> | |
| 66 <param name="type" type="select" label="Plot type"> | |
| 67 <option value="density" selected="true">Density</option> | |
| 68 <option value="dispersion">Dispersion</option> | |
| 69 <option value="fpkmSCV">Squared Coefficient of Variation</option> | |
| 70 <option value="scatterMatrix">Scatter Matrix</option> | |
| 71 <option value="boxplot">Boxplot</option> | |
| 72 <option value="scatter">Scatter</option> | |
| 73 <option value="volcano">Volcano</option> | |
| 74 <option value="heatmap">Heatmap</option> | |
| 75 <option value="cluster">Cluster</option> | |
| 76 <option value="expressionplot">Expression Plot</option> | |
| 77 <option value="expressionbarplot">Expression Bar Plot</option> | |
| 78 <option value="mds">MultiDimentional Scaling (MDS) Plot</option> | |
| 79 <option value="pca">Principal Component Analysis (PCA) Plot</option> | |
| 80 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option> | |
| 81 <option value="dendrogram">Dendrogram</option> | |
| 82 </param> | |
| 83 <when value="density"> | |
| 84 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 85 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> | |
| 86 </when> | |
| 87 <when value="mds"> | |
| 88 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
| 89 </when> | |
| 90 <when value="pca"> | |
| 91 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
| 92 </when> | |
| 93 <when value="maplot"> | |
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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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94 <param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff"> |
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Jim Johnson <jj@umn.edu>
parents:
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changeset
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95 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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parents:
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changeset
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96 </param> |
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Jim Johnson <jj@umn.edu>
parents:
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changeset
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97 <param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff"> |
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fdf01b3c1841
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Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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98 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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fdf01b3c1841
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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99 </param> |
| 0 | 100 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/> |
| 101 </when> | |
| 102 <when value="dendrogram"> | |
| 103 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
| 104 </when> | |
| 105 <when value="dispersion"> | |
| 106 </when> | |
| 107 <when value="fpkmSCV"> | |
| 108 </when> | |
| 109 <when value="scatterMatrix"> | |
| 110 </when> | |
| 111 <when value="boxplot"> | |
| 112 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 113 </when> | |
| 114 <when value="scatter"> | |
| 115 <param name="x" type="text" label="Sample name for x axis"/> | |
| 116 <param name="y" type="text" label="Sample name for y axis"/> | |
| 117 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 118 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> | |
| 119 <conditional name="multiple_genes"> | |
| 120 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 121 <when value="T"> | |
| 122 <param name="features" type="select" label="Expression levels to plot?"> | |
| 123 <option value="gene" selected="true">Genes</option> | |
| 124 <option value="isoforms">Isoforms</option> | |
| 125 <option value="tss">TSS</option> | |
| 126 <option value="cds">CDS</option> | |
| 127 </param> | |
| 128 <repeat name="genes" title="Genes"> | |
| 129 <param name="gene_id" type="text" label="Gene ID"/> | |
| 130 </repeat> | |
| 131 </when> | |
| 132 <when value="F"/> | |
| 133 </conditional> | |
| 134 </when> | |
| 135 <when value="volcano"> | |
| 136 <param name="x" type="text" label="First sample name for comparison"/> | |
| 137 <param name="y" type="text" label="Second sample name for comparison"/> | |
| 138 <conditional name="multiple_genes"> | |
| 139 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
| 140 <when value="T"> | |
| 141 <param name="features" type="select" label="Expression levels to plot?"> | |
| 142 <option value="gene" selected="true">Genes</option> | |
| 143 <option value="isoforms">Isoforms</option> | |
| 144 <option value="tss">TSS</option> | |
| 145 <option value="cds">CDS</option> | |
| 146 </param> | |
| 147 <repeat name="genes" title="Genes"> | |
| 148 <param name="gene_id" type="text" label="Gene ID"/> | |
| 149 </repeat> | |
| 150 </when> | |
| 151 <when value="F"/> | |
| 152 </conditional> | |
| 153 </when> | |
| 154 <when value="heatmap"> | |
| 155 <param name="features" type="select" label="Expression levels to plot?"> | |
| 156 <option value="gene" selected="true">Genes</option> | |
| 157 <option value="isoforms">Isoforms</option> | |
| 158 <option value="tss">TSS</option> | |
| 159 <option value="cds">CDS</option> | |
| 160 </param> | |
| 161 <repeat name="genes" title="Genes"> | |
| 162 <param name="gene_id" type="text" label="Gene ID"/> | |
| 163 </repeat> | |
| 164 <param name="clustering" type="select" label="Cluster by"> | |
| 165 <option value="row">Row</option> | |
| 166 <option value="column">Column</option> | |
| 167 <option value="both" selected="true">Both</option> | |
| 168 <option value="none">None</option> | |
| 169 </param> | |
| 170 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 171 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
| 172 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 173 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> | |
| 174 </when> | |
| 175 <when value="cluster"> | |
| 176 <param name="features" type="select" label="Expression levels to plot?"> | |
| 177 <option value="gene" selected="true">Genes</option> | |
| 178 <option value="isoforms">Isoforms</option> | |
| 179 <option value="tss">TSS</option> | |
| 180 <option value="cds">CDS</option> | |
| 181 </param> | |
| 182 <repeat name="genes" title="Genes"> | |
| 183 <param name="gene_id" type="text" label="Gene ID"/> | |
| 184 </repeat> | |
| 185 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> | |
| 186 <param name="iter_max" type="text" value="100" label="Max iterations"/> | |
| 187 </when> | |
| 188 <when value="expressionplot"> | |
| 189 <param name="features" type="select" label="Expression levels to plot?"> | |
| 190 <option value="gene" selected="true">Genes</option> | |
| 191 <option value="isoforms">Isoforms</option> | |
| 192 <option value="tss">TSS</option> | |
| 193 <option value="cds">CDS</option> | |
| 194 </param> | |
| 195 <param name="gene_id" type="text" label="Gene ID"/> | |
| 196 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 197 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM | |
| 198 values for each condition?"/> | |
| 199 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 200 </when> | |
| 201 <when value="expressionbarplot"> | |
| 202 <param name="features" type="select" label="Expression levels to plot?"> | |
| 203 <option value="gene" selected="true">Genes</option> | |
| 204 <option value="isoforms">Isoforms</option> | |
| 205 <option value="tss">TSS</option> | |
| 206 <option value="cds">CDS</option> | |
| 207 </param> | |
| 208 <param name="gene_id" type="text" label="Gene ID"/> | |
| 209 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
| 210 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
| 211 </when> | |
| 212 </conditional> | |
| 213 </repeat> | |
| 214 </inputs> | |
| 215 <stdio> | |
| 216 <exit_code range="1:" level="fatal" description="CummerBund Error" /> | |
| 217 </stdio> | |
| 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
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219 <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> |
| 0 | 220 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> |
| 221 </data> | |
| 222 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> | |
| 223 </outputs> | |
| 224 | |
| 225 <requirements> | |
| 226 <requirement type="binary">R</requirement> | |
| 227 </requirements> | |
| 228 | |
| 229 <!--> | |
| 230 <tests> | |
| 231 <test> | |
| 232 <param name="" value=""/> | |
| 233 <output name="" file=""/> | |
| 234 </test> | |
| 235 </tests> | |
| 236 --> | |
| 237 <configfiles> | |
| 238 <configfile name="script_file"> | |
| 239 | |
| 240 ## Feature Selection ## | |
| 241 get_features <- function(myGenes, f="gene") { | |
| 242 if (f == "isoforms") | |
| 243 return(isoforms(myGenes)) | |
| 244 else if (f == "tss") | |
| 245 return(TSS(myGenes)) | |
| 246 else if (f == "cds") | |
| 247 return(CDS(myGenes)) | |
| 248 else | |
| 249 return(myGenes) | |
| 250 } | |
| 251 | |
| 252 ## Main Function ## | |
| 253 | |
| 254 ## Load cummeRbund library | |
| 255 library("cummeRbund") | |
| 256 | |
| 257 ## Initialize cuff object | |
|
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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
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258 #if $backend_database_source.backend_database_selector == "cuffdiff_output": |
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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
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259 ## Check if gtfFIle and genome are includes |
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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:
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changeset
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260 #set $gtf_link = None |
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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
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261 #if $backend_database_source.reference.include: |
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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
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262 #set $gtf_link = '.'.join(['cuff',$backend_database_source.reference.gtf_file.extension]) |
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263 system('ln -s $backend_database_source.reference.gtf_file $gtf_link') |
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264 #if $backend_database_source.reference.genome.source == 'cached': |
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265 #set $ref_file = $backend_database_source.reference.genome.ref_fasta |
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266 #else |
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267 #set $ref_file = $backend_database_source.reference.genome.ref_file |
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268 #end if |
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269 #end if |
| 0 | 270 cuff <- readCufflinks(dir = "", |
| 271 dbFile = "${output_database}", | |
| 272 geneFPKM = "${genes_fpkm_tracking}", | |
| 273 geneDiff = "${genes_exp}", | |
| 274 isoformFPKM = "${isoforms_fpkm_tracking}", | |
| 275 isoformDiff = "${isoforms_exp}", | |
| 276 TSSFPKM = "${tss_groups_fpkm_tracking}", | |
| 277 TSSDiff = "${tss_groups_exp}", | |
| 278 CDSFPKM = "${cds_fpkm_tracking}", | |
| 279 CDSExpDiff = "${cds_exp_diff}", | |
| 280 CDSDiff = "${cds_diff}", | |
| 281 promoterFile = "${promoters_diff}", | |
| 282 splicingFile = "${splicing_diff}", | |
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283 #if $gtf_link: |
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284 gtfFile = "${gtf_link}", |
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285 genome = "${ref_file}", |
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286 #end if |
| 0 | 287 rebuild = T) |
| 288 #else: | |
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289 cuff <- readCufflinks(dir = "", |
| 0 | 290 dbFile = "${backend_database_source.input_database}", |
| 291 rebuild = F) | |
| 292 #end if | |
| 293 | |
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294 ## Print out info |
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295 print(cuff) |
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296 sink("cuffdb_info.txt") |
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297 print(cuff) |
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298 print("SAMPLES:") |
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299 samples(cuff) |
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300 print("REPLICATES:") |
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301 replicates(cuff) |
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302 print("FEATURES:") |
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303 print(annotation(genes(cuff))) |
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304 sink() |
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305 |
| 0 | 306 #for $i, $p in enumerate($plots, start=1): |
| 307 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) | |
| 308 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) | |
| 309 tryCatch({ | |
| 310 ## Density plot ## | |
| 311 #if $p.plot['type'] == "density": | |
| 312 csDensity(genes(cuff),replicates=$p.plot.replicates) | |
| 313 | |
| 314 ## Dispersion plot ## | |
| 315 #elif $p.plot['type'] == "dispersion": | |
| 316 dispersionPlot(genes(cuff)) | |
| 317 | |
| 318 ## Squared Coefficient of Variation plot ## | |
| 319 #elif $p.plot['type'] == "fpkmSCV": | |
| 320 fpkmSCVPlot(genes(cuff)) | |
| 321 | |
| 322 ## Scatter Matrix ## | |
| 323 #elif $p.plot['type'] == "scatterMatrix": | |
| 324 csScatterMatrix(genes(cuff)) | |
| 325 | |
| 326 ## Boxplot ## | |
| 327 #elif $p.plot['type'] == "boxplot": | |
| 328 csBoxplot(genes(cuff)) | |
| 329 | |
| 330 ## Scatter ## | |
| 331 #elif $p.plot['type'] == "scatter": | |
| 332 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 333 myGeneIds <- c() | |
| 334 #for $g in $p.plot.multiple_genes['genes']: | |
| 335 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 336 #end for | |
| 337 myGenes <- getGenes(cuff, myGeneIds) | |
| 338 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 339 #else | |
| 340 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
| 341 #end if | |
| 342 | |
| 343 ## Volcano ## | |
| 344 #elif $p.plot['type'] == "volcano": | |
| 345 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
| 346 myGeneIds <- c() | |
| 347 #for $g in $p.plot.multiple_genes['genes']: | |
| 348 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 349 #end for | |
| 350 myGenes <- getGenes(cuff, myGeneIds) | |
| 351 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") | |
| 352 #else | |
| 353 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") | |
| 354 #end if | |
| 355 | |
| 356 ## Heatmap ## | |
| 357 #elif $p.plot['type'] == "heatmap": | |
| 358 myGeneIds <- c() | |
| 359 #for $g in $p.plot.genes: | |
| 360 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 361 #end for | |
| 362 myGenes <- getGenes(cuff, myGeneIds) | |
| 363 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") | |
| 364 | |
| 365 ## Cluster ## | |
| 366 #elif $p.plot['type'] == "cluster": | |
| 367 myGeneIds <- c() | |
| 368 #for $g in $p.plot.genes: | |
| 369 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
| 370 #end for | |
| 371 myGenes <- getGenes(cuff, myGeneIds) | |
| 372 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") | |
| 373 | |
| 374 ## Expression Plot ## | |
| 375 #elif $p.plot['type'] == "expressionplot": | |
| 376 myGeneId <- "$p.plot.gene_id" | |
| 377 myGenes <- getGenes(cuff, myGeneId) | |
| 378 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") | |
| 379 | |
| 380 ## Expression Bar Plot ## | |
| 381 #elif $p.plot['type'] == "expressionbarplot": | |
| 382 myGeneId <- "$p.plot.gene_id" | |
| 383 myGenes <- getGenes(cuff, myGeneId) | |
| 384 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") | |
| 385 | |
| 386 ## MDS plot ## | |
| 387 #elif $p.plot['type'] == "mds": | |
| 388 MDSplot(genes(cuff),replicates=$p.plot.replicates) | |
| 389 | |
| 390 ## PCA plot ## | |
| 391 #elif $p.plot['type'] == "pca": | |
| 392 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates) | |
| 393 | |
| 394 ## MAplot plot ## | |
| 395 #elif $p.plot['type'] == "maplot": | |
| 396 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count}) | |
| 397 | |
| 398 ## Dendogram plot ## | |
| 399 #elif $p.plot['type'] == "dendrogram": | |
| 400 csDendro(genes(cuff),replicates=$p.plot.replicates) | |
| 401 #end if | |
| 402 | |
| 403 },error = function(e) {paste("$p.plot['type'] failed: ", e)}) | |
| 404 devname = dev.off() | |
| 405 | |
| 406 #end for | |
| 407 </configfile> | |
| 408 </configfiles> | |
| 409 | |
| 410 <help> | |
| 411 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. | |
| 412 </help> | |
| 413 | |
| 414 </tool> |