Mercurial > repos > iuc > goseq
annotate goseq.xml @ 1:2be7cffafc39 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 027e71072ff901d6b9593b37113c7b1f8b77527b
| author | iuc |
|---|---|
| date | Sun, 11 Jun 2017 08:57:24 -0400 |
| parents | 084d77515343 |
| children | 25e1e7b40e55 |
| rev | line source |
|---|---|
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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1 <tool id="goseq" name="goseq" version="0.2.2"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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2 <description>tests for overrepresented gene categories</description> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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3 <requirements> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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4 <requirement type="package" version="1.3.2">r-optparse</requirement> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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5 <requirement type="package" version="1.22.0">bioconductor-goseq</requirement> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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6 </requirements> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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7 <stdio> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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8 <regex match="Execution halted" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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9 source="both" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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10 level="fatal" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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11 description="Execution halted." /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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12 <regex match="Error in" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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13 source="both" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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14 level="fatal" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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15 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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16 <regex match="Fatal error" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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17 source="both" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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18 level="fatal" |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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19 description="An undefined error occured, please check your input carefully and contact your administrator." /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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20 </stdio> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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21 <command><![CDATA[ |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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22 Rscript '$__tool_directory__'/goseq.r --dge_file '$dge_file' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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23 --length_file '$length_file' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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24 --category_file '$category_file' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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25 #if $methods['wallenius']: |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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26 --wallenius_tab '$wallenius_tab' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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27 #end if |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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28 #if $methods['hypergeometric']: |
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1
2be7cffafc39
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 027e71072ff901d6b9593b37113c7b1f8b77527b
iuc
parents:
0
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29 --nobias_tab '$nobias_tab' |
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0
084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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30 #end if |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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31 --repcnt '$methods.repcnt' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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32 --sampling_tab '$sampling_tab' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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33 --p_adj_method '$p_adj_method' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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34 --use_genes_without_cat '$use_genes_without_cat' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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35 --make_plots '$make_plots' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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36 --length_bias_plot '$length_bias_plot' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
changeset
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37 --sample_vs_wallenius_plot '$sample_vs_wallenius_plot' |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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38 ]]></command> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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39 <inputs> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff
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40 <param name="dge_file" help="A tabular file with gene names in the first column, and TRUE or FALSE in the last column. TRUE means a gene is differentially expressed. See help section for details." label="Differentially expressed gene file" type="data" format="tabular" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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changeset
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41 <param name="length_file" label="Gene length file for length bias correction" help="You can calculate the gene length using the get length and gc content tool" type="data" format="tabular" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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42 <param name="category_file" label="Gene category file" help="You can obtain a mapping of gene id to gene ontology using the getgo tool" type="data" format="tabular" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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43 <param name="use_genes_without_cat" 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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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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44 label="Count genes without any category?" type="boolean"/> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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45 <section name="methods" title="Method options" expanded="True"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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46 <param name="wallenius" type="boolean" checked="true" label="Use wallenius method" help="See help for details" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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47 <param name="hypergeometric" type="boolean" checked="false" label="Use hypergeometric method" help="Does not use gene length information. See help for details" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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48 <param name="repcnt" help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" size="3" type="integer" min="0" max="10000" value="0" /> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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49 </section> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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50 <param name="p_adj_method" type="select" label="Select a method for multiple hypothesis testing correction"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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51 <option value="BH" selected="true">Benjamini-Hochberg [FDR] (1995)</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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52 <option value="holm">Holm (1979)</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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53 <option value="hommel">Hommel (1988)</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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54 <option value="hochberg">Hochberg (1988)</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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55 <option value="bonferroni">Bonferroni</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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56 <option value="BY">Benjamini - Yekutieli (2001)</option> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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57 </param> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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58 <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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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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59 </inputs> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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60 <outputs> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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61 <data name="length_bias_plot" format="pdf" label="length bias plot"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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62 <filter>make_plots</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
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63 <filter>methods['hypergeometric']</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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64 </data> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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65 <data name="sample_vs_wallenius_plot" format="pdf" label="Plot P-value from sampling against wallenius distribution"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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66 <filter>methods['repcnt'] != 0</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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67 <filter>methods['wallenius']</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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68 <filter>make_plots</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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69 </data> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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70 <data name="nobias_tab" format="tabular" label="Ranked category list - no length bias correction"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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71 <filter>methods['hypergeometric']</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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72 </data> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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73 <data name="sampling_tab" format="tabular" label="Ranked category list - sampling"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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74 <filter>methods['repcnt'] != 0</filter> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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75 </data> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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76 <data name="wallenius_tab" format="tabular" label="Ranked category list - wallenius method"> |
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084d77515343
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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77 <filter>methods['wallenius']</filter> |
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78 </data> |
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79 </outputs> |
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80 <tests> |
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81 <test> |
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82 <param name="dge_file" value="dge_list.tab" ftype="tabular"/> |
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83 <param name="length_file" value="gene_length.tab" ftype="tabular"/> |
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84 <param name="category_file" value="category.tab" ftype="tabular"/> |
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85 <param name="use_genes_without_cat" value="true" /> |
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86 <output name="wallenius_tab" file="wal.tab" compare="re_match"/> |
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87 </test> |
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88 </tests> |
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89 <help> |
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90 |
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91 **What it does** |
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92 |
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93 Detects Gene Ontology and/or other user defined categories which are over/under-represented in RNA-seq data. |
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94 |
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95 Options map closely to the excellent manual_ |
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96 |
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97 |
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98 **Input files** |
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99 |
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100 *DGE list:* |
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101 goseq needs a tabular file with genes in the first column, and TRUE or FALSE in the last column. |
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102 TRUE means the gene should count as differentially expressed, FALSE means it is not differentially expressed. |
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103 You can use the "Compute an expression on every row" tool to create a TRUE / FALSE column for your dataset. |
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104 |
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105 *Gene length file:* |
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106 goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes |
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107 using a prodbability weight function (PWF). |
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108 The format of this file is tabular, with gene_id in the first column and length in the second column. |
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109 The "get length and gc content" tool can produce such a file. |
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110 |
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111 *Gene category file:* |
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112 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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113 category identifier in the second column. |
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114 |
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115 **Method options** |
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116 |
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117 3 methods, "Wallenius", "Sampling" and "Hypergeometric", can be used to calculate the p-values as follows. |
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118 |
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119 *"Wallenius"* approximates the true distribution of numbers of members of a category amongst DE genes by the Wallenius non-central hypergeometric distribution. |
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120 This distribution assumes that within a category all genes have the same probability of being chosen. |
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121 Therefore, this approximation works best when the range in probabilities obtained by the probability weighting function is small. |
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122 |
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123 *"Sampling"* uses random sampling to approximate the true distribution and uses it to calculate the p-values for over (and under) representation of categories. |
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124 Although this is the most accurate method given a high enough value of sampling depth, its use quickly becomes computationally prohibitive. |
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125 |
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126 *"Hypergeometric"* assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution. |
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127 Useful if you wish to test the effect of selection bias on your results. |
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128 |
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129 CAUTION: "Hypergeometric" should NEVER be used for producing results for biological interpretation. |
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130 If there is genuinely no bias in power to detect DE in your experiment, the PWF will reflect this and the other methods will produce accuracte results. |
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131 |
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132 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf |
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133 |
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134 |
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135 </help> |
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136 <citations> |
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137 <citation type="doi">10.1186/gb-2010-11-2-r14</citation> |
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138 </citations> |
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139 </tool> |