Mercurial > repos > yhoogstrate > edger_with_design_matrix
diff edgeR_Convert_DGE_Table_to_Bedgraph.xml @ 108:a02794bb9073 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
| author | yhoogstrate |
|---|---|
| date | Tue, 01 Sep 2015 04:45:24 -0400 |
| parents | 450c1c9a2938 |
| children | f871dff92e7c |
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--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 04:32:16 2015 -0400 +++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Sep 01 04:45:24 2015 -0400 @@ -1,90 +1,93 @@ <?xml version="1.0" encoding="UTF-8"?> - <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0"> - <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description> - - <requirements> - <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement> - </requirements> - - <command interpreter="python"> - edger_dge_table_to_bedgraph - -t $cpm_table - -g $geneset - - #if $logfc: - -c3 $logfc - #end if - - #if $logcpm: - -c4 $logcpm - #end if - - #if $lr: - -c5 $lr - #end if - - #if $pvalue: - -c6 $pvalue - #end if - - #if $fdr: - -c7 $fdr - #end if - </command> - - <inputs> - <param format="tabular" name="cpm_table" type="data" label="'differentially expressed genes'-table as result from EdgeR" help="must have 7 columns of which the 2nd are gene names matching the GTF file" /> - <param format="gtf,gff,gff3" name="geneset" type="data" label="Geneset used for estimating expression levels prior to expression analysis" /> - - <param name="columns" type="select" label="Desired columns" multiple="true" display="checkboxes"> - <option value="c3" selected="true">logFC</option> - <option value="c4">logCPM</option> - <option value="c5">LR</option> - <option value="c6">PValue</option> - <option value="c7" selected="true">FDR</option> - </param> - </inputs> - - <outputs> - <data format="bedgraph" name="logfc" label="logFC from ${cpm_table.name}"> - <filter>"c3" in columns</filter> - </data> - - <data format="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}"> - <filter>"c4" in columns</filter> - </data> - - <data format="bedgraph" name="lr" label="LR from ${cpm_table.name}"> - <filter>"c5" in columns</filter> - </data> - - <data format="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}"> - <filter>"c6" in columns</filter> - </data> - - <data format="bedgraph" name="fdr" label="FDR from ${cpm_table.name}"> - <filter>"c7" in columns</filter> - </data> - </outputs> - - <tests> - <test> - <param name="cpm_table" value="Convert_DGE_Table_to_Bedgraph/table_01.tabular.txt" /> - <param name="geneset" value="Convert_DGE_Table_to_Bedgraph/genes_01.gtf" /> - - <param name="columns" value="c3,c7" /> - - <output name="logfc" file="Convert_DGE_Table_to_Bedgraph/logFC.output.bedgraph" /> - <output name="fdr" file="Convert_DGE_Table_to_Bedgraph/FDR.output.bedgraph" /> - </test> - </tests> - - <help> - P-values and FDRs are swapped from 1 to 0, and 0 to 1, because this way the most siginificant genes will obtain the highest values which is convenient for visualisation. - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btp616</citation> - <citation type="doi">10.1093/bioinformatics/btt688</citation> - </citations> + <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0"> + <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description> + + <macros> + <import>edgeR_macros.xml</import> + </macros> + + <requirements> + <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement> + </requirements> + + <command interpreter="python"> + edger_dge_table_to_bedgraph + -t $cpm_table + -g $geneset + + #if $logfc: + -c3 $logfc + #end if + + #if $logcpm: + -c4 $logcpm + #end if + + #if $lr: + -c5 $lr + #end if + + #if $pvalue: + -c6 $pvalue + #end if + + #if $fdr: + -c7 $fdr + #end if + </command> + + <inputs> + <param format="tabular" name="cpm_table" type="data" label="'differentially expressed genes'-table as result from EdgeR" help="must have 7 columns of which the 2nd are gene names matching the GTF file" /> + <param format="gtf,gff,gff3" name="geneset" type="data" label="Geneset used for estimating expression levels prior to expression analysis" /> + + <param name="columns" type="select" label="Desired columns" multiple="true" display="checkboxes"> + <option value="c3" selected="true">logFC</option> + <option value="c4">logCPM</option> + <option value="c5">LR</option> + <option value="c6">PValue</option> + <option value="c7" selected="true">FDR</option> + </param> + </inputs> + + <outputs> + <data format="bedgraph" name="logfc" label="logFC from ${cpm_table.name}"> + <filter>"c3" in columns</filter> + </data> + + <data format="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}"> + <filter>"c4" in columns</filter> + </data> + + <data format="bedgraph" name="lr" label="LR from ${cpm_table.name}"> + <filter>"c5" in columns</filter> + </data> + + <data format="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}"> + <filter>"c6" in columns</filter> + </data> + + <data format="bedgraph" name="fdr" label="FDR from ${cpm_table.name}"> + <filter>"c7" in columns</filter> + </data> + </outputs> + + <tests> + <test> + <param name="cpm_table" value="Convert_DGE_Table_to_Bedgraph/table_01.tabular.txt" /> + <param name="geneset" value="Convert_DGE_Table_to_Bedgraph/genes_01.gtf" /> + + <param name="columns" value="c3,c7" /> + + <output name="logfc" file="Convert_DGE_Table_to_Bedgraph/logFC.output.bedgraph" /> + <output name="fdr" file="Convert_DGE_Table_to_Bedgraph/FDR.output.bedgraph" /> + </test> + </tests> + + <help> + P-values and FDRs are swapped from 1 to 0, and 0 to 1, because this way the most siginificant genes will obtain the highest values which is convenient for visualisation. + + @CONTACT@ + </help> + + <expand macro="citations" /> </tool>