Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/loadMultiFastqFiles.xml @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
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| 1 <tool id="load_multiFASTQFiles" name="load_multiFASTQfiles" > | |
| 2 <description>To load several FASTQ files from different conditions.</description> | |
| 3 <command interpreter="python"> loadMultiFastqFiles.py -o $multiFASTQfiles_out | |
| 4 #if $single_end_paired_end.mapping_mode == 'single': | |
| 5 -i | |
| 6 #for $i in $single_end_paired_end.condition_groups | |
| 7 #for $j in $i.replicates | |
| 8 $j.fastq_file | |
| 9 #end for | |
| 10 @ | |
| 11 #end for | |
| 12 | |
| 13 #elif $single_end_paired_end.mapping_mode == 'paired': | |
| 14 | |
| 15 --pairedEnd $multiFASTQfiles_paired_end_out | |
| 16 -i | |
| 17 #for $i in $single_end_paired_end.condition_groups | |
| 18 #for $j in $i.replicates | |
| 19 $j.fastq_file | |
| 20 @@ | |
| 21 $j.fastq_paired_end_file | |
| 22 #end for | |
| 23 @ | |
| 24 #end for | |
| 25 #end if | |
| 26 | |
| 27 </command> | |
| 28 <inputs> | |
| 29 <conditional name="single_end_paired_end"> | |
| 30 <param name="mapping_mode" type="select" label="The uploading fastq files for single-end or paired-end mapping mode."> | |
| 31 <option value="single">Single-End</option> | |
| 32 <option value="paired">Paire-End</option> | |
| 33 </param> | |
| 34 <when value="single"> | |
| 35 <repeat name="condition_groups" title="Condition group" min="2"> | |
| 36 <repeat name="replicates" title="Replicate"> | |
| 37 <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/> | |
| 38 </repeat> | |
| 39 </repeat> | |
| 40 </when> | |
| 41 <when value="paired"> | |
| 42 <repeat name="condition_groups" title="Condition group" min="2"> | |
| 43 <repeat name="replicates" title="Replicate"> | |
| 44 <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/> | |
| 45 <param name="fastq_paired_end_file" format="fastq" type="data" label="fastq paired end complementary file" help="Add the corresponding paired end file for paired end mapping"/> | |
| 46 </repeat> | |
| 47 </repeat> | |
| 48 </when> | |
| 49 | |
| 50 </conditional> | |
| 51 </inputs> | |
| 52 | |
| 53 <outputs> | |
| 54 <data format="txt" name="multiFASTQfiles_out" label="loadMultiFASTQFiles result" help="This program gives you a list of files you choose for the following data analysis."/> | |
| 55 <data format="txt" name="multiFASTQfiles_paired_end_out" label="loadMultiFASTQFiles for paired end result" help="This program gives you a list of files you choose for the following data analysis."> | |
| 56 <filter>(single_end_paired_end['mapping_mode']=='paired')</filter> | |
| 57 | |
| 58 </data> | |
| 59 </outputs> | |
| 60 <help> | |
| 61 **This tool is to help upload several data for differential expression pipeline. Before click 'Execute', you should Click** Ctrl + here_ **first to open the pipeline in a new page.** | |
| 62 | |
| 63 .. _here: http://127.0.0.1:8085/u/yufei-luo/w/differentialexpressiondeseq-with-replicates | |
| 64 </help> | |
| 65 | |
| 66 </tool> | |
| 67 | |
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