Mercurial > repos > artbio > ngsplot
changeset 1:4dd92ce61a5c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n'
| author | artbio |
|---|---|
| date | Fri, 08 Dec 2017 09:25:05 -0500 |
| parents | 3ca58369469c |
| children | 4b4d858c0aa9 |
| files | ngsplot.xml runNGSplot.pl |
| diffstat | 2 files changed, 6 insertions(+), 2168 deletions(-) [+] |
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line diff
--- a/ngsplot.xml Wed Dec 06 19:01:53 2017 -0500 +++ b/ngsplot.xml Fri Dec 08 09:25:05 2017 -0500 @@ -11,6 +11,7 @@ <command><![CDATA[ export NGSPLOT="$__tool_directory__" && +printenv && #if $numsamples.numsamples2 == "1": perl "$__tool_directory__"/runNGSplot.pl $genome_name @@ -879,7 +880,7 @@ <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="2">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> @@ -887,7 +888,7 @@ <option value="7">7</option> <option value="8">8</option> <option value="9">9</option> - <option value="10">10</option> + <option value="10">10</option> --> </param> <when value="1"> @@ -940,2166 +941,6 @@ </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>
--- a/runNGSplot.pl Wed Dec 06 19:01:53 2017 -0500 +++ b/runNGSplot.pl Fri Dec 08 09:25:05 2017 -0500 @@ -22,7 +22,7 @@ my $randfile2 = $randfile; $randfile2 =~ s/config\.txt/logfile/gm; -my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile"); +my $outfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.config.txt"); open(FILE,">$outfile"); for (my $i=1;$i<=$numsamples;$i++) { @@ -87,7 +87,7 @@ $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS"; } -my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2"); +my $logfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.log"); open(FILE2,">>$logfile"); my $cmd5="pwd >> $logfile 2>&1"; system($cmd5); @@ -112,17 +112,14 @@ print("$cmd\n"); my $cmd2="cp data.zip $O"; my $cmd3="rm $outfile"; -my $cmd4="rm $logfile"; syswrite(FILE2, "\n$cmd\n"); syswrite(FILE2, "\n$cmd2\n"); syswrite(FILE2, "\n$cmd3\n"); -syswrite(FILE2, "\n$cmd4\n\n"); # print STDERR "cmd: $cmd\n"; system($cmd); system($cmd2); -#system($cmd3); -#system($cmd4); +system($cmd3); close(FILE2);