Mercurial > repos > ngsplot > ngsplot
diff 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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngsplot_galaxytoolshed_v.10/ngsplot_main/ngsplot.xml Tue Mar 31 10:15:27 2015 -0400 @@ -0,0 +1,3175 @@ +<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>