Mercurial > repos > ngsplot > ngsplot
diff ngsplot_galaxytoolshed_v1.0/ngsplot_main/ngsplot.xml @ 12:f7debdafc7cb draft default tip
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author | ngsplot |
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date | Tue, 31 Mar 2015 10:15:27 -0400 |
parents | 896dfca167fb |
children |
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--- a/ngsplot_galaxytoolshed_v1.0/ngsplot_main/ngsplot.xml Thu Mar 19 17:39:23 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3175 +0,0 @@ -<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>