Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate goseq.xml @ 5:b79c65c90744 draft

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author mvdbeek
date Sun, 28 Feb 2016 11:52:10 -0500
parents 76eab486aba9
children 0e9424413ab0
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mvdbeek
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1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.5">
0
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2 <description />
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3 <requirements>
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4 <requirement type="package" version="3.2.1">R</requirement>
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5 <requirement type="package" version="1.22.0">goseq</requirement>
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6 </requirements>
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7 <command interpreter="Rscript">
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8 goseq.r --dge_file "$dge_file"
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9 --p_adj_column "$p_adj_column"
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10 --cutoff "$p_adj_cutoff"
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11 #if $source.use_length_file == "yes":
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12 --length_file "$length_file"
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13 #end if
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14 --genome "$genome"
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15 --gene_id "$gene_id"
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16 --wallenius_tab "$wallenius_tab"
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17 --sampling_tab "$sampling_tab"
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18 --nobias_tab "$nobias_tab"
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19 --length_bias_plot "$length_bias_plot"
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20 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
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21 --repcnt "$repcnt"
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22 --use_genes_without_cat "$use_genes_without_cat"
0
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23 </command>
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24 <inputs>
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25 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
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26 <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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27 <param help="A boolean to indicate whether genes without a categorie should still be used. 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"
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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28 name="use_genes_without_cat" label="Count genes without any category" type="boolean"/>
0
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29 <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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30 <conditional name="source">
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31 <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select">
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32 <option value="no">no</option>
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33 <option value="yes">yes</option>
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34 </param>
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35 <when value="yes">
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36 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
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37 </when>
2
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38 <when value="no">
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39 </when>
0
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40 </conditional>
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41 <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
1
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42 <options from_data_table="go_genomes"></options>
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43 </param>
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44 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
1
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45 <options from_data_table="go_gene_ids"></options>
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46 </param>
2
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47 <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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48 </inputs>
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49 <outputs>
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50 <data format="pdf" label="length bias plot" name="length_bias_plot" />
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51 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
2
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52 <filter>repcnt != 0</filter>
0
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53 </data>
3
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54 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
0
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55 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
2
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56 <filter>repcnt != 0</filter>
0
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57 </data>
3
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58 <data format="tabular" label="Ranked category list - wallenius approx. of p-values" name="wallenius_tab" />
0
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59 </outputs>
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60 <tests>
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61 <test>
2
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62 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
0
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63 <param name="use_length_file" value="no" />
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64 <param name="p_adj_column" value="2" />
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65 <param name="genome" value="hg19" />
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66 <param name="gene_id" value="ensGene" />
2
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67 <output name="wallenius_tab" file="wall.tab" compare="contains"/>/>
0
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68 </test>
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69 </tests>
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70 <help>
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71
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72 **What it does**
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73
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74 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
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75
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76 Options map closely to the excellent manual_
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78 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
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80
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81 </help>
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82 <citations>
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83 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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84 </citations>
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85 </tool>