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view ngsplot_galaxytoolshed_v.10/ngsplot_main/ngsplot.xml @ 12:f7debdafc7cb draft default tip
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| author | ngsplot |
|---|---|
| date | Tue, 31 Mar 2015 10:15:27 -0400 |
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<tool id="ngs.plot" name="ngs.plot"> <command interpreter="perl"> #if $numsamples.numsamples2 == "1": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "2": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "3": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "4": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "5": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "6": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $numsamples.usepair.bamfile6 $numsamples.usepair.reffile6 $numsamples.usepair.genelist6.usegenelist6 $numsamples.usepair.genelist6.genelist6 $numsamples.usepair.title6 $numsamples.usepair.fraglen6 $numsamples.usepair.linecol6 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "7": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $numsamples.usepair.bamfile6 $numsamples.usepair.reffile6 $numsamples.usepair.genelist6.usegenelist6 $numsamples.usepair.genelist6.genelist6 $numsamples.usepair.title6 $numsamples.usepair.fraglen6 $numsamples.usepair.linecol6 $numsamples.usepair.bamfile7 $numsamples.usepair.reffile7 $numsamples.usepair.genelist7.usegenelist7 $numsamples.usepair.genelist7.genelist7 $numsamples.usepair.title7 $numsamples.usepair.fraglen7 $numsamples.usepair.linecol7 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "8": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $numsamples.usepair.bamfile6 $numsamples.usepair.reffile6 $numsamples.usepair.genelist6.usegenelist6 $numsamples.usepair.genelist6.genelist6 $numsamples.usepair.title6 $numsamples.usepair.fraglen6 $numsamples.usepair.linecol6 $numsamples.usepair.bamfile7 $numsamples.usepair.reffile7 $numsamples.usepair.genelist7.usegenelist7 $numsamples.usepair.genelist7.genelist7 $numsamples.usepair.title7 $numsamples.usepair.fraglen7 $numsamples.usepair.linecol7 $numsamples.usepair.bamfile8 $numsamples.usepair.reffile8 $numsamples.usepair.genelist8.usegenelist8 $numsamples.usepair.genelist8.genelist8 $numsamples.usepair.title8 $numsamples.usepair.fraglen8 $numsamples.usepair.linecol8 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "9": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $numsamples.usepair.bamfile6 $numsamples.usepair.reffile6 $numsamples.usepair.genelist6.usegenelist6 $numsamples.usepair.genelist6.genelist6 $numsamples.usepair.title6 $numsamples.usepair.fraglen6 $numsamples.usepair.linecol6 $numsamples.usepair.bamfile7 $numsamples.usepair.reffile7 $numsamples.usepair.genelist7.usegenelist7 $numsamples.usepair.genelist7.genelist7 $numsamples.usepair.title7 $numsamples.usepair.fraglen7 $numsamples.usepair.linecol7 $numsamples.usepair.bamfile8 $numsamples.usepair.reffile8 $numsamples.usepair.genelist8.usegenelist8 $numsamples.usepair.genelist8.genelist8 $numsamples.usepair.title8 $numsamples.usepair.fraglen8 $numsamples.usepair.linecol8 $numsamples.usepair.bamfile9 $numsamples.usepair.reffile9 $numsamples.usepair.genelist9.usegenelist9 $numsamples.usepair.genelist9.genelist9 $numsamples.usepair.title9 $numsamples.usepair.fraglen9 $numsamples.usepair.linecol9 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #else if $numsamples.numsamples2 == "10": runNGSplot.pl $genome_name $genomic_region_source_type.genomic_region $genomic_region_source_type.further_information $genomic_region_source_type.interval_size $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size $numsamples.numsamples2 $numsamples.usepair.usepair1 $numsamples.usepair.bamfile1 $numsamples.usepair.reffile1 $numsamples.usepair.genelist1.usegenelist1 $numsamples.usepair.genelist1.genelist1 $numsamples.usepair.title1 $numsamples.usepair.fraglen1 $numsamples.usepair.linecol1 $numsamples.usepair.bamfile2 $numsamples.usepair.reffile2 $numsamples.usepair.genelist2.usegenelist2 $numsamples.usepair.genelist2.genelist2 $numsamples.usepair.title2 $numsamples.usepair.fraglen2 $numsamples.usepair.linecol2 $numsamples.usepair.bamfile3 $numsamples.usepair.reffile3 $numsamples.usepair.genelist3.usegenelist3 $numsamples.usepair.genelist3.genelist3 $numsamples.usepair.title3 $numsamples.usepair.fraglen3 $numsamples.usepair.linecol3 $numsamples.usepair.bamfile4 $numsamples.usepair.reffile4 $numsamples.usepair.genelist4.usegenelist4 $numsamples.usepair.genelist4.genelist4 $numsamples.usepair.title4 $numsamples.usepair.fraglen4 $numsamples.usepair.linecol4 $numsamples.usepair.bamfile5 $numsamples.usepair.reffile5 $numsamples.usepair.genelist5.usegenelist5 $numsamples.usepair.genelist5.genelist5 $numsamples.usepair.title5 $numsamples.usepair.fraglen5 $numsamples.usepair.linecol5 $numsamples.usepair.bamfile6 $numsamples.usepair.reffile6 $numsamples.usepair.genelist6.usegenelist6 $numsamples.usepair.genelist6.genelist6 $numsamples.usepair.title6 $numsamples.usepair.fraglen6 $numsamples.usepair.linecol6 $numsamples.usepair.bamfile7 $numsamples.usepair.reffile7 $numsamples.usepair.genelist7.usegenelist7 $numsamples.usepair.genelist7.genelist7 $numsamples.usepair.title7 $numsamples.usepair.fraglen7 $numsamples.usepair.linecol7 $numsamples.usepair.bamfile8 $numsamples.usepair.reffile8 $numsamples.usepair.genelist8.usegenelist8 $numsamples.usepair.genelist8.genelist8 $numsamples.usepair.title8 $numsamples.usepair.fraglen8 $numsamples.usepair.linecol8 $numsamples.usepair.bamfile9 $numsamples.usepair.reffile9 $numsamples.usepair.genelist9.usegenelist9 $numsamples.usepair.genelist9.genelist9 $numsamples.usepair.title9 $numsamples.usepair.fraglen9 $numsamples.usepair.linecol9 $numsamples.usepair.bamfile10 $numsamples.usepair.reffile10 $numsamples.usepair.genelist10.usegenelist10 $numsamples.usepair.genelist10.genelist10 $numsamples.usepair.title10 $numsamples.usepair.fraglen10 $numsamples.usepair.linecol10 $gene_database $randomly_sample $GO.gene_order $GO.KNC $GO.MIT $GO.NRS $chunk_size $quality_requirement $standard_error $radius_size $flooding_fraction $smooth_method $shaded_area $out_zip $out_avg_png $out_hm_png #end if: </command> <!--> <--> <inputs> <param type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" > </param> <conditional name="genomic_region_source_type"> <param type="select" name="genomic_region" label="Genomic region" help=""> <option value="tss">TSS</option> <option value="tes">TES</option> <option value="genebody">Genebody</option> <option value="exon">Exon</option> <option value="cgi">CGI</option> <option value="bed">Customized bed file</option> </param> <when value="tss"> <param type="select" name="further_information" label="Further information: Not required for TSS"> <option value="na">Not Required</option> </param> <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS"> <option value="na">Not Required</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option--> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <!--when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when--> </conditional> </when> <when value="tes"> <param type="select" name="further_information" label="Further information: Not required for TES"> <option value="na">Not Required</option> </param> <param name="interval_size" type="select" label="Interval Region Size: Not required for TES"> <option value="na">Not Required</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option--> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <!--when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when--> </conditional> </when> <when value="genebody"> <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot"> <option value="chipseq">ChIP-seq</option> <option value="rnaseq">RNA-seq</option> </param> <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> <option value="automatic">Default</option> <option value="0">Small</option> <option value="1">Large</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> </when> <when value="exon"> <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot"> <option value="canonical">Canonical</option> <option value="variant">Variant</option> <option value="promoter">Promoter</option> <option value="polyA">polyA</option> <option value="altAcceptor">altAcceptor</option> <option value="altDonor">altDonor</option> <option value="altBoth">altBoth</option> </param> <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> <option value="automatic">Default</option> <option value="0">Small</option> <option value="1">Large</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> </when> <when value="cgi"> <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot"> <option value="ProximalPromoter">ProximalPromoter</option> <option value="Genebody">GeneBody</option> <option value="Genedesert">GeneDesert</option> <option value="OtherIntergenic">OtherIntergenic</option> <option value="Pericentromere">Pericentromere</option> <option value="Subtelomere">Subtelomere</option> <option value="Promoter1k">Promoter1k</option> <option value="Promoter3k">Promoter3k</option> </param> <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> <option value="automatic">Default</option> <option value="0">Small</option> <option value="1">Large</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> </when> <when value="bed"> <param type="select" name="further_information" label="Further information: Not required for bed input"> <option value="na">Not Required</option> </param> <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region."> <option value="automatic">Default</option> <option value="0">Small</option> <option value="1">Large</option> </param> <conditional name="flanking_region_option_source_type"> <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region"> <option value="flanking_region_size">Specify flanking region size in base pairs</option> <option value="flanking_floating_size">Specify fractional size with respect to interval size</option> </param> <when value="flanking_region_size"> <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/> </when> <when value="flanking_floating_size"> <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/> </when> </conditional> </when> </conditional> <conditional name="numsamples"> <param type="select" name="numsamples2" label="Number of samples to plot"> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> <option value="9">9</option> <option value="10">10</option> </param> <when value="1"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 1 sample, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 1 sample, no refpairs, entry 1--> </when> <when value="yes"> <!-- START: 1 sample, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 1 sample, yes refpairs, entry 1--> </when> </conditional> </when> <when value="2"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 2 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 2 samples, no refpairs, entry 1--> <!-- START: 2 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 2 samples, no refpairs, entry 2--> </when> <when value="yes"> <!-- START: 2 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 2 samples, yes refpairs, entry 1--> <!-- START: 2 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 2 samples, yes refpairs, entry 2--> </when> </conditional> </when> <when value="3"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 3 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 3 samples, no refpairs, entry 1--> <!-- START: 3 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 3 samples, no refpairs, entry 2--> <!-- START: 3 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 3 samples, no refpairs, entry 3--> </when> <when value="yes"> <!-- START: 3 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 3 samples, yes refpairs, entry 1--> <!-- START: 3 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 3 samples, yes refpairs, entry 2--> <!-- START: 3 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 3 samples, yes refpairs, entry 2--> </when> </conditional> </when> <when value="4"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 4 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 4 samples, no refpairs, entry 1--> <!-- START: 4 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 4 samples, no refpairs, entry 2--> <!-- START: 4 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 4 samples, no refpairs, entry 3--> <!-- START: 4 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 4 samples, no refpairs, entry 4--> </when> <when value="yes"> <!-- START: 4 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 4 samples, yes refpairs, entry 1--> <!-- START: 4 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 4 samples, yes refpairs, entry 2--> <!-- START: 4 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 4 samples, yes refpairs, entry 3--> <!-- START: 4 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 4 samples, yes refpairs, entry 4--> </when> </conditional> </when> <when value="5"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 5 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 5 samples, no refpairs, entry 1--> <!-- START: 5 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 5 samples, no refpairs, entry 2--> <!-- START: 5 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 5 samples, no refpairs, entry 3--> <!-- START: 5 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 5 samples, no refpairs, entry 4--> <!-- START: 5 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 5 samples, no refpairs, entry 5--> </when> <when value="yes"> <!-- START: 5 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 5 samples, yes refpairs, entry 1--> <!-- START: 5 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 5 samples, yes refpairs, entry 2--> <!-- START: 5 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 5 samples, yes refpairs, entry 3--> <!-- START: 5 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 5 samples, yes refpairs, entry 4--> <!-- START: 5 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 5 samples, yes refpairs, entry 5--> </when> </conditional> </when> <when value="6"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 6 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 1--> <!-- START: 6 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 2--> <!-- START: 6 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 3--> <!-- START: 6 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 4--> <!-- START: 6 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 5--> <!-- START: 6 samples, no refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="hidden" name="reffile6" value="na"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 6 samples, no refpairs, entry 6--> </when> <when value="yes"> <!-- START: 6 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 1--> <!-- START: 6 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 2--> <!-- START: 6 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 3--> <!-- START: 6 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 4--> <!-- START: 6 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 5--> <!-- START: 6 samples, yes refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 6 samples, yes refpairs, entry 6--> </when> </conditional> </when> <when value="7"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 7 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 1--> <!-- START: 7 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 2--> <!-- START: 7 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 3--> <!-- START: 7 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 4--> <!-- START: 7 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 5--> <!-- START: 7 samples, no refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="hidden" name="reffile6" value="na"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 6--> <!-- START: 7 samples, no refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="hidden" name="reffile7" value="na"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 7 samples, no refpairs, entry 7--> </when> <when value="yes"> <!-- START: 7 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 1--> <!-- START: 7 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 2--> <!-- START: 7 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 3--> <!-- START: 7 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 4--> <!-- START: 7 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 5--> <!-- START: 7 samples, yes refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 6--> <!-- START: 7 samples, yes refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 7 samples, yes refpairs, entry 7--> </when> </conditional> </when> <when value="8"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 8 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 1--> <!-- START: 8 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 2--> <!-- START: 8 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 3--> <!-- START: 8 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 4--> <!-- START: 8 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 5--> <!-- START: 8 samples, no refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="hidden" name="reffile6" value="na"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 6--> <!-- START: 8 samples, no refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="hidden" name="reffile7" value="na"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 7--> <!-- START: 8 samples, no refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="hidden" name="reffile8" value="na"/> <conditional name="genelist7"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 8 samples, no refpairs, entry 8--> </when> <when value="yes"> <!-- START: 8 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 1--> <!-- START: 8 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 2--> <!-- START: 8 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 3--> <!-- START: 8 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 4--> <!-- START: 8 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 5--> <!-- START: 8 samples, yes refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 6--> <!-- START: 8 samples, yes refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 7--> <!-- START: 8 samples, yes refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> <conditional name="genelist8"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 8 samples, yes refpairs, entry 8--> </when> </conditional> </when> <when value="9"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 9 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 1--> <!-- START: 9 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 2--> <!-- START: 9 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 3--> <!-- START: 9 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 4--> <!-- START: 9 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 5--> <!-- START: 9 samples, no refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="hidden" name="reffile6" value="na"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 6--> <!-- START: 9 samples, no refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="hidden" name="reffile7" value="na"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 7--> <!-- START: 9 samples, no refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="hidden" name="reffile8" value="na"/> <conditional name="genelist8"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 8--> <!-- START: 9 samples, no refpairs, entry 9--> <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> <param type="hidden" name="reffile9" value="na"/> <conditional name="genelist9"> <param type="select" name="usegenelist9" label="Sample 9: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist9" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> <!-- END: 9 samples, no refpairs, entry 9--> </when> <when value="yes"> <!-- START: 9 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 1--> <!-- START: 9 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 2--> <!-- START: 9 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 3--> <!-- START: 9 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 4--> <!-- START: 9 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 5--> <!-- START: 9 samples, yes refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 6--> <!-- START: 9 samples, yes refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 7--> <!-- START: 9 samples, yes refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> <conditional name="genelist8"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 8--> <!-- START: 9 samples, yes refpairs, entry 9--> <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/> <conditional name="genelist9"> <param type="select" name="usegenelist9" label="Sample 9: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist9" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> <!-- END: 9 samples, yes refpairs, entry 9--> </when> </conditional> </when> <when value="10"> <conditional name="usepair"> <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities."> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> <!-- START: 10 samples, no refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="hidden" name="reffile1" value="na"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 1--> <!-- START: 10 samples, no refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="hidden" name="reffile2" value="na"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 2--> <!-- START: 10 samples, no refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="hidden" name="reffile3" value="na"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 3--> <!-- START: 10 samples, no refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="hidden" name="reffile4" value="na"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 4--> <!-- START: 10 samples, no refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="hidden" name="reffile5" value="na"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 5--> <!-- START: 10 samples, no refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="hidden" name="reffile6" value="na"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 6--> <!-- START: 10 samples, no refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="hidden" name="reffile7" value="na"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 7--> <!-- START: 10 samples, no refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="hidden" name="reffile8" value="na"/> <conditional name="genelist8"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 8--> <!-- START: 10 samples, no refpairs, entry 9--> <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> <param type="hidden" name="reffile9" value="na"/> <conditional name="genelist9"> <param type="select" name="usegenelist9" label="Sample 9: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist9" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 9--> <!-- START: 10 samples, no refpairs, entry 10--> <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/> <param type="hidden" name="reffile10" value="na"/> <conditional name="genelist10"> <param type="select" name="usegenelist10" label="Sample 10: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist10" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/> <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/> <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/> <!-- END: 10 samples, no refpairs, entry 10--> </when> <when value="yes"> <!-- START: 10 samples, yes refpairs, entry 1--> <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/> <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/> <conditional name="genelist1"> <param type="select" name="usegenelist1" label="Sample 1: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist1" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/> <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/> <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 1--> <!-- START: 10 samples, yes refpairs, entry 2--> <param type="data" name="bamfile2" label="Sample 2: Input BAM file"/> <param type="data" name="reffile2" label="Sample 2: Reference BAM file"/> <conditional name="genelist2"> <param type="select" name="usegenelist2" label="Sample 2: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist2" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist2" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title2" value="plot2" label="Sample 2: Image title"/> <param type="text" name="fraglen2" value="150" label="Sample 2: Expected fragment length"/> <param type="text" name="linecol2" value="blue" label="Sample 2: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 2--> <!-- START: 10 samples, yes refpairs, entry 3--> <param type="data" name="bamfile3" label="Sample 3: Input BAM file"/> <param type="data" name="reffile3" label="Sample 3: Reference BAM file"/> <conditional name="genelist3"> <param type="select" name="usegenelist3" label="Sample 3: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist3" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist3" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title3" value="plot3" label="Sample 3: Image title"/> <param type="text" name="fraglen3" value="150" label="Sample 3: Expected fragment length"/> <param type="text" name="linecol3" value="red" label="Sample 3: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 3--> <!-- START: 10 samples, yes refpairs, entry 4--> <param type="data" name="bamfile4" label="Sample 4: Input BAM file"/> <param type="data" name="reffile4" label="Sample 4: Reference BAM file"/> <conditional name="genelist4"> <param type="select" name="usegenelist4" label="Sample 4: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist4" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist4" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title4" value="plot4" label="Sample 4: Image title"/> <param type="text" name="fraglen4" value="150" label="Sample 4: Expected fragment length"/> <param type="text" name="linecol4" value="pink" label="Sample 4: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 4--> <!-- START: 10 samples, yes refpairs, entry 5--> <param type="data" name="bamfile5" label="Sample 5: Input BAM file"/> <param type="data" name="reffile5" label="Sample 5: Reference BAM file"/> <conditional name="genelist5"> <param type="select" name="usegenelist5" label="Sample 5: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist5" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist5" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title5" value="plot5" label="Sample 5: Image title"/> <param type="text" name="fraglen5" value="150" label="Sample 5: Expected fragment length"/> <param type="text" name="linecol5" value="slateblue" label="Sample 5: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 5--> <!-- START: 10 samples, yes refpairs, entry 6--> <param type="data" name="bamfile6" label="Sample 6: Input BAM file"/> <param type="data" name="reffile6" label="Sample 6: Reference BAM file"/> <conditional name="genelist6"> <param type="select" name="usegenelist6" label="Sample 6: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist6" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist6" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title6" value="plot6" label="Sample 6: Image title"/> <param type="text" name="fraglen6" value="150" label="Sample 6: Expected fragment length"/> <param type="text" name="linecol6" value="sienna" label="Sample 6: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 6--> <!-- START: 10 samples, yes refpairs, entry 7--> <param type="data" name="bamfile7" label="Sample 7: Input BAM file"/> <param type="data" name="reffile7" label="Sample 7: Reference BAM file"/> <conditional name="genelist7"> <param type="select" name="usegenelist7" label="Sample 7: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist7" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist7" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title7" value="plot7" label="Sample 7: Image title"/> <param type="text" name="fraglen7" value="150" label="Sample 7: Expected fragment length"/> <param type="text" name="linecol7" value="tomato" label="Sample 7: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 7--> <!-- START: 10 samples, yes refpairs, entry 8--> <param type="data" name="bamfile8" label="Sample 8: Input BAM file"/> <param type="data" name="reffile8" label="Sample 8: Reference BAM file"/> <conditional name="genelist8"> <param type="select" name="usegenelist8" label="Sample 8: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist8" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist8" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title8" value="plot8" label="Sample 8: Image title"/> <param type="text" name="fraglen8" value="150" label="Sample 8: Expected fragment length"/> <param type="text" name="linecol8" value="turquoise" label="Sample 8: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 8--> <!-- START: 10 samples, yes refpairs, entry 9--> <param type="data" name="bamfile9" label="Sample 9: Input BAM file"/> <param type="data" name="reffile9" label="Sample 9: Reference BAM file"/> <conditional name="genelist9"> <param type="select" name="usegenelist9" label="Sample 9: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist9" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist9" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title9" value="plot9" label="Sample 9: Image title"/> <param type="text" name="fraglen9" value="150" label="Sample 9: Expected fragment length"/> <param type="text" name="linecol9" value="violetred" label="Sample 9: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 9--> <!-- START: 10 samples, yes refpairs, entry 10--> <param type="data" name="bamfile10" label="Sample 10: Input BAM file"/> <param type="data" name="reffile10" label="Sample 10: Reference BAM file"/> <conditional name="genelist10"> <param type="select" name="usegenelist10" label="Sample 10: Gene list"> <option value="no">Plot whole genome</option> <option value="yes">Provide restricted gene list</option> </param> <when value="no"> <param type="hidden" name="genelist10" value="-1"/> </when> <when value="yes"> <param type="data" name="genelist10" label="Choose the uploaded gene list for plotting"/> </when> </conditional> <param type="text" name="title10" value="plot10" label="Sample 10: Image title"/> <param type="text" name="fraglen10" value="150" label="Sample 10: Expected fragment length"/> <param type="text" name="linecol10" value="tan3" label="Sample 10: Line plot color"/> <!-- END: 10 samples, yes refpairs, entry 10--> </when> </conditional> </when> </conditional> <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl"> <option value="ensembl">Ensembl</option> <option value="refseq">RefSeq</option> </param> <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/> <conditional name="GO"> <param type="select" name="gene_order" label="Gene order algorithm"> <option value="total">Overall enrichment of the 1st profile</option> <option value="hc">Hierarchical clustering</option> <option value="max">Peak value of the 1st profile</option> <option value="prod">Product of all profiles on the same region</option> <option value="diff">Difference between the 1st and 2nd profiles</option> <option value="km">K-means clustering</option> <option value="none">No ranking algorithm applied. Use order in gene list.</option> </param> <when value="km"> <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/> <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/> <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/> </when> <when value="total"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> <when value="hc"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> <when value="max"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> <when value="prod"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> <when value="diff"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> <when value="none"> <param type="hidden" name="KNC" value="NA" /> <param type="hidden" name="MIT" value="NA" /> <param type="hidden" name="NRS" value="NA" /> </when> </conditional> <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/> <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/> <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve."> <option value="1">Yes</option> <option value="0">No</option> </param> <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/> <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/> <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles"> <option value="1">No</option> <option value="3">Slightly</option> <option value="5">Somewhat</option> <option value="9">Quite</option> <option value="13">Super</option> </param> <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/> <!-- --> </inputs> <help></help> <outputs> <data format="pdf" name="out_avg_png" /> <data format="pdf" name="out_hm_png" /> <data format="zip" name="out_zip"/> </outputs> </tool>