Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison goseq.xml @ 0:fe71b97cc1a5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 85e0f34aec3045f48ca9b1a00db02de199a99c95-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 24 Feb 2016 15:54:37 -0500 |
| parents | |
| children | 1b03f6232900 |
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| -1:000000000000 | 0:fe71b97cc1a5 |
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| 1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.1"> | |
| 2 <description /> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.2.1">R</requirement> | |
| 5 <requirement type="package" version="1.22.0">goseq</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="Rscript"> | |
| 8 goseq.r --dge_file "$dge_file" | |
| 9 --p_adj_column "$p_adj_column" | |
| 10 --cutoff "$p_adj_cutoff" | |
| 11 --genome "$genome" | |
| 12 --gene_id "$gene_id" | |
| 13 --wallenius_tab "$wallenius_tab" | |
| 14 --sampling_tab "$sampling_tab" | |
| 15 --nobias_tab "$nobias_tab" | |
| 16 --length_bias_plot "$length_bias_plot" | |
| 17 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot" | |
| 18 --repcnt "$repcnt" | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" /> | |
| 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"/> | |
| 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" /> | |
| 24 <param help="Needed to retrive gene length for length correction" label="Select the genome source" name="genome" size="3" type="select"> | |
| 25 <options from_file="genomes.loc"> | |
| 26 <column name="value" index="0"/> | |
| 27 <column name="name" index="1"/> | |
| 28 </options> | |
| 29 </param> | |
| 30 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select"> | |
| 31 <options from_file="gene_ids.loc"> | |
| 32 <column name="value" index="0"/> | |
| 33 <column name="name" index="1"/> | |
| 34 </options> | |
| 35 </param> | |
| 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" /> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" /> | |
| 40 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab" /> | |
| 41 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> | |
| 42 <data format="pdf" label="length bias plot" name="length_bias_plot" /> | |
| 43 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot" /> | |
| 44 </outputs> | |
| 45 <tests> | |
| 46 <test> | |
| 47 | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 51 | |
| 52 **What it does** | |
| 53 | |
| 54 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. | |
| 55 | |
| 56 Options map closely to the excellent manual_ | |
| 57 | |
| 58 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf | |
| 59 | |
| 60 | |
| 61 </help> | |
| 62 <citations> | |
| 63 <citation type="doi">10.1186/gb-2010-11-2-r14</citation> | |
| 64 </citations> | |
| 65 </tool> |