ngsplot: ngsplot.xml annotate

annotate ngsplot.xml @ 4:9652d08d8441 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit 73a8ef46dddb0a1b224720bcdfe46050ee9a1b8b

author	artbio
date	Tue, 26 Dec 2017 08:07:56 -0500
parents	de27d4172d19
children

rev	line source
4 9652d08d8441 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit 73a8ef46dddb0a1b224720bcdfe46050ee9a1b8b artbio parents: 3 diff changeset	1 <tool id="ngsplot" name="ngsplot" version="0.3.1">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	2 <description>visualize NGS samples at functional genomic regions - beta</description>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	3 <requirements>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	4 <requirement type="package" version="1.17.1=r3.3.2_1">r-catools</requirement>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	5 <requirement type="package" version="1.3.4">r-domc</requirement>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	6 <requirement type="package" version="1.42.0">bioconductor-bsgenome</requirement>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	7 <!-- <requirement type="package" version="1.26.1">bioconductor-rsamtools</requirement> -->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	8 <requirement type="package" version="1.32.0">bioconductor-shortread</requirement>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	9 <!-- <requirement type="package" version="0.16.1=r3.2.2_0">bioconductor-biocgenerics</requirement> -->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	10 </requirements>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	11
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	12 <command><![CDATA[
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	13 export NGSPLOT="$__tool_directory__" &&
1 4dd92ce61a5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n' artbio parents: 0 diff changeset	14 printenv &&
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	15 #if $numsamples.numsamples2 == "1":
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	16 perl "$__tool_directory__"/runNGSplot.pl
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	17 $genome_name
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	18 $genomic_region_source_type.genomic_region
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	19 $genomic_region_source_type.further_information
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	20 $genomic_region_source_type.interval_size
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	21 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	22 $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	23 $numsamples.numsamples2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	24 $numsamples.usepair.usepair1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	25
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	26 $numsamples.usepair.bamfile1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	27 $numsamples.usepair.reffile1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	28 $numsamples.usepair.genelist1.usegenelist1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	29 $numsamples.usepair.genelist1.genelist1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	30 $numsamples.usepair.title1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	31 $numsamples.usepair.fraglen1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	32 $numsamples.usepair.linecol1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	33
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	34 $gene_database
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	35 $randomly_sample
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	36 $GO.gene_order
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	37 $GO.KNC
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	38 $GO.MIT
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	39 $GO.NRS
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	40 $chunk_size
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	41 $quality_requirement
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	42 $standard_error
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	43 $radius_size
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	44 $flooding_fraction
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	45 $smooth_method
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	46 $shaded_area
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	47 ## $out_zip
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	48 $out_avg_png $out_hm_png &&
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	49 tar -cf $out_tar data/
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	50 #end if
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	51
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	52 ]]></command>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	53
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	54 <!-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	55 <-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	56
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	57 <inputs>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	58 <param type="select" name="genome_name" label="Genome" help="Select Genome (only hg38 supported in this draft)">
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	59 <option value="hg38">hg38</option>
4 9652d08d8441 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit 73a8ef46dddb0a1b224720bcdfe46050ee9a1b8b artbio parents: 3 diff changeset	60 <option value="mm9">mm9</option>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	61 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	62 <conditional name="genomic_region_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	63 <param type="select" name="genomic_region" label="Genomic region" help="">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	64 <option value="tss">TSS</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	65 <option value="tes">TES</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	66 <option value="genebody">Genebody</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	67 <option value="exon">Exon</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	68 <option value="cgi">CGI</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	69 <option value="bed">Customized bed file</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	70 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	71
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	72 <when value="tss">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	73 <param type="select" name="further_information" label="Further information: Not required for TSS">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	74 <option value="na">Not Required</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	75 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	76 <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	77 <option value="na">Not Required</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	78 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	79 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	80 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	81 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	82 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	83 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	84 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	85 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	86 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	87 <!--when value="flanking_floating_size">
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	88 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	89 </when-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	90 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	91 </when>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	92 <when value="tes">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	93 <param type="select" name="further_information" label="Further information: Not required for TES">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	94 <option value="na">Not Required</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	95 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	96 <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	97 <option value="na">Not Required</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	98 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	99 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	100 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	101 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	102 <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	103 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	104 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	105 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	106 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	107 <!--when value="flanking_floating_size">
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	108 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	109 </when-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	110 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	111 </when>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	112 <when value="genebody">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	113 <param type="select" name="further_information" label="You selected Genebody, further information can be provided for specific regions to plot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	114 <option value="chipseq">ChIP-seq</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	115 <option value="rnaseq">RNA-seq</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	116 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	117 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	118 <option value="automatic">Default</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	119 <option value="0">Small</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	120 <option value="1">Large</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	121 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	122 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	123 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	124 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	125 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	126 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	127 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	128 <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	129 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	130 <when value="flanking_floating_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	131 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	132 </when>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	133 </conditional>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	134 </when>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	135 <when value="exon">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	136 <param type="select" name="further_information" label="You selected Exon, further information can be provided for specific regions to plot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	137 <option value="canonical">Canonical</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	138 <option value="variant">Variant</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	139 <option value="promoter">Promoter</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	140 <option value="polyA">polyA</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	141 <option value="altAcceptor">altAcceptor</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	142 <option value="altDonor">altDonor</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	143 <option value="altBoth">altBoth</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	144 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	145 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	146 <option value="automatic">Default</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	147 <option value="0">Small</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	148 <option value="1">Large</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	149 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	150 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	151 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	152 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	153 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	154 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	155 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	156 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	157 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	158 <when value="flanking_floating_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	159 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	160 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	161 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	162 </when>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	163 <when value="cgi">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	164 <param type="select" name="further_information" label="You select CGI, further information can be provided for specific regions to plot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	165 <option value="ProximalPromoter">ProximalPromoter</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	166 <option value="Genebody">GeneBody</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	167 <option value="Genedesert">GeneDesert</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	168 <option value="OtherIntergenic">OtherIntergenic</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	169 <option value="Pericentromere">Pericentromere</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	170 <option value="Subtelomere">Subtelomere</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	171 <option value="Promoter1k">Promoter1k</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	172 <option value="Promoter3k">Promoter3k</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	173 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	174 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	175 <option value="automatic">Default</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	176 <option value="0">Small</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	177 <option value="1">Large</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	178 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	179 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	180 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	181 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	182 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	183 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	184 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	185 <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	186 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	187 <when value="flanking_floating_size">
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	188 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	189 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	190 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	191 </when>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	192 <when value="bed">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	193 <param type="select" name="further_information" label="Further information: Not required for bed input">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	194 <option value="na">Not Required</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	195 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	196 <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	197 <option value="automatic">Default</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	198 <option value="0">Small</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	199 <option value="1">Large</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	200 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	201 <conditional name="flanking_region_option_source_type">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	202 <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	203 <option value="flanking_region_size">Specify flanking region size in base pairs</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	204 <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	205 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	206 <when value="flanking_region_size">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	207 <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	208 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	209 <when value="flanking_floating_size">
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	210 <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	211 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	212 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	213 </when>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	214 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	215
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	216
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	217 <conditional name="numsamples">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	218 <param type="select" name="numsamples2" label="Number of samples to plot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	219 <option value="1">1</option>
1 4dd92ce61a5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n' artbio parents: 0 diff changeset	220 <!-- <option value="2">2</option>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	221 <option value="3">3</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	222 <option value="4">4</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	223 <option value="5">5</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	224 <option value="6">6</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	225 <option value="7">7</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	226 <option value="8">8</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	227 <option value="9">9</option>
1 4dd92ce61a5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n' artbio parents: 0 diff changeset	228 <option value="10">10</option> -->
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	229 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	230
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	231 <when value="1">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	232 <conditional name="usepair">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	233 <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.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	234 <option value="no">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	235 <option value="yes">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	236 </param>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	237 <when value="no">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	238 <!-- START: 1 sample, no refpairs, entry 1-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	239 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	240 <param type="hidden" name="reffile1" value="na"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	241 <conditional name="genelist1">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	242 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	243 <option value="no">Plot whole genome</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	244 <option value="yes">Provide restricted gene list</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	245 </param>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	246 <when value="no">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	247 <param type="hidden" name="genelist1" value="-1"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	248 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	249 <when value="yes">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	250 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	251 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	252 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	253 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	254 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	255 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	256 <!-- END: 1 sample, no refpairs, entry 1-->
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	257 </when>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	258 <when value="yes">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	259 <!-- START: 1 sample, yes refpairs, entry 1-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	260 <param type="data" name="bamfile1" label="Sample 1: Input BAM file"/>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	261 <param type="data" name="reffile1" label="Sample 1: Reference BAM file"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	262 <conditional name="genelist1">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	263 <param type="select" name="usegenelist1" label="Sample 1: Gene list">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	264 <option value="no">Plot whole genome</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	265 <option value="yes">Provide restricted gene list</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	266 </param>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	267 <when value="no">
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	268 <param type="hidden" name="genelist1" value="-1"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	269 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	270 <when value="yes">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	271 <param type="data" name="genelist1" label="Choose the uploaded gene list for plotting"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	272 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	273 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	274 <param type="text" name="title1" value="plot1" label="Sample 1: Image title"/>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	275 <param type="text" name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>
de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	276 <param type="text" name="linecol1" value="green" label="Sample 1: Line plot color"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	277 <!-- END: 1 sample, yes refpairs, entry 1-->
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	278 </when>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	279 </conditional>
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	280 </when>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	281 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	282
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	283
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	284
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	285 <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	286 <option value="ensembl">Ensembl</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	287 <option value="refseq">RefSeq</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	288 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	289 <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	290 <conditional name="GO">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	291 <param type="select" name="gene_order" label="Gene order algorithm">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	292 <option value="total">Overall enrichment of the 1st profile</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	293 <option value="hc">Hierarchical clustering</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	294 <option value="max">Peak value of the 1st profile</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	295 <option value="prod">Product of all profiles on the same region</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	296 <option value="diff">Difference between the 1st and 2nd profiles</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	297 <option value="km">K-means clustering</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	298 <option value="none">No ranking algorithm applied. Use order in gene list.</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	299 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	300 <when value="km">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	301 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	302 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	303 <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	304 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	305 <when value="total">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	306 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	307 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	308 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	309 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	310 <when value="hc">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	311 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	312 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	313 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	314 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	315 <when value="max">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	316 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	317 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	318 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	319 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	320 <when value="prod">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	321 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	322 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	323 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	324 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	325 <when value="diff">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	326 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	327 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	328 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	329 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	330 <when value="none">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	331 <param type="hidden" name="KNC" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	332 <param type="hidden" name="MIT" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	333 <param type="hidden" name="NRS" value="NA" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	334 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	335 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	336 <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	337 <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	338 <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	339 <option value="1">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	340 <option value="0">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	341 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	342
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	343 <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	344 <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	345 <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	346 <option value="1">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	347 <option value="3">Slightly</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	348 <option value="5">Somewhat</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	349 <option value="9">Quite</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	350 <option value="13">Super</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	351 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	352 <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	353 <!--
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	354 -->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	355 </inputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	356
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	357 <help></help>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	358 <outputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	359 <data format="pdf" name="out_avg_png" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	360 <data format="pdf" name="out_hm_png" />
3 de27d4172d19 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n' artbio parents: 2 diff changeset	361 <data format="tar" name="out_tar"/>
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	362 </outputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	363 </tool>

Mercurial > repos > artbio > ngsplot

annotate ngsplot.xml @ 4:9652d08d8441 draft default tip