Mercurial > repos > yhoogstrate > edger_with_design_matrix
view edgeR_Concatenate_Expression_Matrices.xml @ 84:ddcc677fb13d draft
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author | yhoogstrate |
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date | Wed, 19 Nov 2014 09:45:17 -0500 |
parents | b2738b4d7c8c |
children | 46745f5666ac |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0"> <description>Create a full expression matrix by selecting the desired columns from specific count tables</description> <command> #set $j = 0 #set $paste = [] #if $add_geneids.choice == "true": #set $filename = str($j)+".txt" #set paste = paste + [$filename] cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ; #set $j += 1 #end if #for $sample in $samples: ##echo "$sample.column_index" ##echo "$sample.column_index.value" #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value]) #set $filename = str($j)+".txt" #set paste = paste + [$filename] cut -f "$column_str" "$sample.sample" > $filename ; #set $j += 1 #end for #if $add_lengths.choice == "true": #set $filename = str($j)+".txt" #set paste = paste + [$filename] cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ; #set $j += 1 #end if #set $paste_str = " ".join([str(x).strip() for x in $paste]) paste $paste_str > $expression_matrix </command> <inputs> <conditional name="add_geneids"> <param name="choice" type="select" label="Add a gene-IDs column at the end of the file" help="Highly recommended to select!" > <option value="false">No</option> <option value="true" selected="true">Yes</option> </param> <when value="false" /> <when value="true"> <param name="sample_geneids" type="data" format="tabular" label="Select Read-count dataset that contains a column for GeneIDs" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> <param name="column_geneids" numerical="false" use_header_names="true" label="Select GeneID column" type="data_column" data_ref="sample_geneids" multiple="false"> <validator type="no_options" message="Please select at least one column." /> </param> </when> </conditional> <repeat name="samples" title="Expression Table" help="E.g. a earlier concatenated table, or a HT-seq, featureCounts or DESeq-count result."> <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> <!-- select columns --> <param name="column_index" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample" multiple="true" size="120" display="checkboxes"> <validator type="no_options" message="Please select at least one column." /> </param> </repeat> <conditional name="add_lengths"> <param name="choice" type="select" label="Add a gene-lengths column at the end of the file" help="Optional, only usefull if RPKM/FPKM calculation is desired." > <option value="false">No</option> <option value="true">Yes</option> </param> <when value="false" /> <when value="true"> <param name="sample_lengths" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." /> <param name="column_lengths" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample_lengths" multiple="false" size="120"> <validator type="no_options" message="Please select at least one column." /> </param> </when> </conditional> <param name="remove_comment_lines" type="boolean" label="Automatically remove 'comment' lines starting with a '#'" truevale="true" falsevalue="false" selected="true" help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." /> </inputs> <outputs> <data format="tabular" name="expression_matrix" label="Expression matrix" /> </outputs> <tests> <test> <param name="add_geneids.choice" value="true" /> <param name="choice" value="true" /> <param name="add_geneids" value="true" /> <!-- Add a gene-IDs column at the end of the file true Select Read-count dataset that contains a column for GeneIDs 21: MCF7_featureCounts_E2.txt Select GeneID column 1 Read-count dataset that belongs to a pair 14: MCF7_featureCounts_Control_1.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 15: MCF7_featureCounts_Control_2.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 16: MCF7_featureCounts_Control_3.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 17: MCF7_featureCounts_Control_4.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 18: MCF7_featureCounts_Control_5.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 22: MCF7_featureCounts_Control_6.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 20: MCF7_featureCounts_Control_7.txt Select columns that are associated with this factor level 2 Read-count dataset that belongs to a pair 21: MCF7_featureCounts_E2.txt Select columns that are associated with this factor level 2 3 4 5 6 7 8 Add a gene-lengths column at the end of the file true Read-count dataset that belongs to a pair 26: MCF7_featureCounts_GeneLengths.txt Select columns that are associated with this factor level 2 Automatically remove 'comment' lines starting with a '#' False --> <output name="expression_matrix" file="MCF7_featureCounts_concatenated.txt" /> </test> </tests> <help> edgeR: Concatenate Expression Matrices ####################################### Overview -------- Create subsets from or combined expression matrices. **Notes** Make sure the tables have an identical number of columns compared to the number of headers. If you export tables using R, make sure you set: col.names=NA. Otherwise column may be swapped during concatenation. Input ----- Contact ------- The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: http://toolshed.dtls.nl/ http://toolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu/ </help> </tool>