Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate goseq.xml @ 6:0e9424413ab0 draft

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author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents b79c65c90744
children 9ffae7bc23c2
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6
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1 <tool id="goseq" name="goseq" version="0.2.0">
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2 <description>tests for overrepresented gene categories</description>
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3 <macros>
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4 <import>go_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command interpreter="Rscript">
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9 goseq.r --dge_file "$dge_file"
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10 --p_adj_column "$p_adj_column"
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11 --cutoff "$p_adj_cutoff"
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12 --length_file "$length_file"
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13 --category_file "$category_file"
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14 --wallenius_tab "$wallenius_tab"
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15 --sampling_tab "$sampling_tab"
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16 --nobias_tab "$nobias_tab"
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17 --length_bias_plot "$length_bias_plot"
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18 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
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19 --repcnt "$repcnt"
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20 --use_genes_without_cat "$use_genes_without_cat"
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21 --make_plots "$make_plots"
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22 </command>
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23 <inputs>
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24 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
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25 <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" numeric="true" data_ref="dge_file"/>
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26 <param label="Gene length file for length bias correction" help="You can calculate the gene length using the get length and gc content tool" name="length_file" type="data" format="tabular" required="true" />
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27 <param label="Gene category file" help="You can obtain a mapping of gene id to gene ontology using the getgo tool" name="category_file" type="data" format="tabular" required="true" />
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28 <param help="For example, a large number of gene may have no GO term annotated. If this option is set to FALSE, those genes will be ignored in the calculation of p-values. If this option is set to TRUE, then these genes will count towards the total number of genes outside the category being tested"
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29 name="use_genes_without_cat" label="Count genes without any category?" type="boolean"/>
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30 <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
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31 <param help="These plots may help you compare the different p-value estimation methods that goseq can use." label="Produce diagnostic plots?" name="make_plots" type="boolean"></param>
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32 <param help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" />
0
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33 </inputs>
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34 <outputs>
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35 <data format="pdf" label="length bias plot" name="length_bias_plot">
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36 <filter>make_plots</filter>
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37 </data>
0
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38 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
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39 <filter>repcnt != 0</filter>
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40 <filter>make_plots</filter>
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41 </data>
3
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42 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
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43 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
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44 <filter>repcnt != 0</filter>
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45 </data>
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46 <data format="tabular" label="Ranked category list - wallenius approx. of p-values" name="wallenius_tab" />
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47 </outputs>
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48 <tests>
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49 <test>
2
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50 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
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51 <param name="length_file" value="gene_length.tab" ftype="tabular"/>
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52 <param name="category_file" value="category.tab" ftype="tabular"/>
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53 <param name="use_genes_without_cat" value="true" />
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54 <param name="p_adj_column" value="2" />
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55 <output name="wallenius_tab" file="wal.tab" compare="contains"/>/>
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56 </test>
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57 </tests>
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58 <help>
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60 **What it does**
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61
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62 Detects Gene Ontology and/or other user defined categories which are over/under-represented in RNA-seq data.
0
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64 Options map closely to the excellent manual_
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65
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67 **Input files**
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69 goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes.
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70 The format of this file is tabular, with gene_id in the first column and length in the second column.
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71 The "get length and gc content" tool can produce such a file.
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73 You will also need a file describing the membership of genes in categories. The format of this file is gene_id in the first column,
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74 category name in the second column. If you are interested in gene ontology categories you can use the getgo file to retrive
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75 gene ontologies for model organisms, or you can construct your own file.
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76
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77 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
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79
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80 </help>
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81 <citations>
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82 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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83 </citations>
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84 </tool>