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1 <tool id="load_multiFASTQFiles" name="load_multiFASTQfiles" >
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2 <description>To load several FASTQ files from different conditions.</description>
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3 <command interpreter="python"> loadMultiFastqFiles.py -o $multiFASTQfiles_out
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4 #if $single_end_paired_end.mapping_mode == 'single':
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5 -i
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6 #for $i in $single_end_paired_end.condition_groups
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7 #for $j in $i.replicates
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8 $j.fastq_file
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9 #end for
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10 @
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11 #end for
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12
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13 #elif $single_end_paired_end.mapping_mode == 'paired':
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14
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15 --pairedEnd $multiFASTQfiles_paired_end_out
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16 -i
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17 #for $i in $single_end_paired_end.condition_groups
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18 #for $j in $i.replicates
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19 $j.fastq_file
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20 @@
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21 $j.fastq_paired_end_file
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22 #end for
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23 @
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24 #end for
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25 #end if
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26
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27 </command>
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28 <inputs>
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29 <conditional name="single_end_paired_end">
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30 <param name="mapping_mode" type="select" label="The uploading fastq files for single-end or paired-end mapping mode.">
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31 <option value="single">Single-End</option>
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32 <option value="paired">Paire-End</option>
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33 </param>
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34 <when value="single">
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35 <repeat name="condition_groups" title="Condition group" min="2">
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36 <repeat name="replicates" title="Replicate">
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37 <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
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38 </repeat>
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39 </repeat>
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40 </when>
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41 <when value="paired">
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42 <repeat name="condition_groups" title="Condition group" min="2">
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43 <repeat name="replicates" title="Replicate">
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44 <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
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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"/>
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46 </repeat>
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47 </repeat>
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48 </when>
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49
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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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."/>
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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.">
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56 <filter>(single_end_paired_end['mapping_mode']=='paired')</filter>
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57
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58 </data>
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59 </outputs>
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60 <help>
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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.**
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62
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63 .. _here: http://127.0.0.1:8085/u/yufei-luo/w/differentialexpressiondeseq-with-replicates
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64 </help>
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65
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66 </tool>
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