Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate goseq.xml @ 1:3ab168143b69 draft

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author mvdbeek
date Thu, 25 Feb 2016 05:26:51 -0500
parents fe71b97cc1a5
children 1b03f6232900
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fe71b97cc1a5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 85e0f34aec3045f48ca9b1a00db02de199a99c95-dirty
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1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.1">
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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 "$p_adj_cutoff"
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11 --genome "$genome"
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12 --gene_id "$gene_id"
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13 --wallenius_tab "$wallenius_tab"
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14 --sampling_tab "$sampling_tab"
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15 --nobias_tab "$nobias_tab"
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16 --length_bias_plot "$length_bias_plot"
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17 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
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18 --repcnt "$repcnt"
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19 </command>
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20 <inputs>
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21 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
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22 <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" data_ref="dge_file"/>
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23 <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider gene differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
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24 <param help="Needed to retrive gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
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25 <options from_file="genomes.loc">
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26 <column name="value" index="0"/>
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27 <column name="name" index="1"/>
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28 </options>
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29 </param>
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30 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
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31 <options from_file="gene_ids.loc">
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32 <column name="value" index="0"/>
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33 <column name="name" index="1"/>
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34 </options>
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35 </param>
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36 <param help="Do this many random samplings. Larger values take a long time" label="Number of random sampling" name="repcnt" size="3" type="integer" min="100" max="10000" value="1000" />
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37 </inputs>
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38 <outputs>
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39 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
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40 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab" />
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41 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
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42 <data format="pdf" label="length bias plot" name="length_bias_plot" />
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43 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot" />
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44 </outputs>
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45 <tests>
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46 <test>
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47
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48 </test>
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49 </tests>
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50 <help>
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51
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52 **What it does**
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53
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54 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
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55
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56 Options map closely to the excellent manual_
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57
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58 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
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59
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60
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
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64 </citations>
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65 </tool>