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Changeset 46:4d2a8f98a502 (2019-01-28)

Previous changeset 45:942eea8359fe (2017-12-08) Next changeset 47:9ba44c15cad1 (2019-06-18)

Commit message:
Uploaded

modified:
complete.sh
complete_immunerepertoire.xml
igblast/igblast.sh
imgt_loader/imgt_loader.r
imgt_loader/imgt_loader.sh
report_clonality/IGH_junctie_analyse.png
report_clonality/RScript.r
report_clonality/genes.txt
report_clonality/jquery-1.11.0.min.js
report_clonality/naive_cdr3_char.htm
report_clonality/naive_circos.htm
report_clonality/naive_clonality.htm
report_clonality/naive_compare.htm
report_clonality/naive_downloads.htm
report_clonality/naive_gene_freq.htm
report_clonality/naive_heatmap.htm
report_clonality/naive_junction.htm
report_clonality/naive_overview.htm
report_clonality/r_wrapper.sh
report_clonality/style.css
report_clonality/tabber.js

added:
LICENSE
README.md

removed:
igblastparser/igparse.pl
report_clonality/circos/LTe50046.ttf
report_clonality/circos/LTe50048.ttf
report_clonality/circos/LTe50050.ttf
report_clonality/circos/LTe50054.ttf
report_clonality/circos/fonts.conf~
report_clonality/circos/housekeeping.conf~
report_clonality/circos/pragmata.ttf
report_clonality/circos/wingding.ttf
tool_dependencies.xml

diff -r 942eea8359fe -r 4d2a8f98a502 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Mon Jan 28 09:37:41 2019 -0500

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 David van Zessen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
\ No newline at end of file

diff -r 942eea8359fe -r 4d2a8f98a502 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Jan 28 09:37:41 2019 -0500

[

@@ -0,0 +1,122 @@
+# ARGalaxy Immune Repertoire
+This is the GitHub repository for the ARGalaxy Immune repertoire pipeline.
+The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c).
+
+## Overview
+
+In execution order:
+
+#### imgt_loader or igblast
+
+###### imgt_loader (Recommended)
+Start the analysis with [IMGT HighV Quest](https://www.imgt.org/HighV-QUEST/) archives.
+An IMGT archive file holds [multiple tabular files](http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#output3), this script extracts the specific columns relevant to the analysis from several of these files.
+
+`Rscript imgt_loader.r 1_Summary.txt 3_Nt-sequences.txt 5_AA-sequences.txt 6_Junction.txt 4_IMGT-gapped-AA-sequences.txt /path/to/output.txt`
+
+
+###### igblast
+Start the analysis with FASTA files that are aligned with [igblast](https://www.ncbi.nlm.nih.gov/igblast/).
+Note that this method will provide less information than the IMGT archive.
+
+`sh igblast.sh /path/to/sequences.fasta species locus /path/to/output.txt`
+
+#### experimental_design
+This script will merge multiple result files (from the last step) into a single file with an additional ID and Replicate column to differentiate the individual samples during the analysis and to allow for analysis across samples.
+
+`Rscript experimental_design.r /path/to/input_1 id_1 [/path/to/input_2 id_2] [/path/to/input_n id_n] /path/to/output`
+
+#### report_clonality
+The R script that creates the analysis result.
+
+`sh r_wrapper.sh /path/to/experimental_design/output.txt /path/to/output_dir/output.html /path/to/output_dir "clonaltype" "species" "locus" "filter_productive" "clonality_method"`
+
+###### parameters
+Clonaltype:
+- none
+- Top.V.Gene,CDR3.Seq
+- Top.V.Gene,CDR3.Seq.DNA
+- Top.V.Gene,Top.J.Gene,CDR3.Seq
+- Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA
+- Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA
+
+Species:
+- Homo sapiens functional
+- Homo sapiens
+- Homo sapiens non-functional
+- Bos taurus
+- Bos taurus functional
+- Bos taurus non-functional
+- Camelus dromedarius
+- Camelus dromedarius functional
+- Camelus dromedarius non-functional
+- Canis lupus familiaris
+- Canis lupus familiaris functional
+- Canis lupus familiaris non-functional
+- Danio rerio
+- Danio rerio functional
+- Danio rerio non-functional
+- Macaca mulatta
+- Macaca mulatta functional
+- Macaca mulatta non-functional
+- Mus musculus
+- Mus musculus functional
+- Mus musculus non-functional
+- Mus spretus
+- Mus spretus functional
+- Mus spretus non-functional
+- Oncorhynchus mykiss
+- Oncorhynchus mykiss functional
+- Oncorhynchus mykiss non-functional
+- Ornithorhynchus anatinus
+- Ornithorhynchus anatinus functional
+- Ornithorhynchus anatinus non-functional
+- Oryctolagus cuniculus
+- Oryctolagus cuniculus functional
+- Oryctolagus cuniculus non-functional
+- Rattus norvegicus
+- Rattus norvegicus functional
+- Rattus norvegicus non-functional
+- Sus scrofa
+- Sus scrofa functional
+- Sus scrofa non-functional
+
+Locus:
+- TRA
+- TRD
+- TRG
+- TRB
+- IGH
+- IGI
+- IGK
+- IGL
+
+Filter productive:
+- yes
+- no
+
+Clonality Method:
+- none
+- old
+- boyd
+
+## complete.sh
+This script will run all of the above for you, it will detect if you are using FASTA files or IMGT archives and use the appropriate tools.
+
+`sh complete.sh /path/to/input_1 id_1 [/path/to/input_n id_n] /path/to/out_dir/out.html /path/to/out_dir clonaltype species locus filter_productive clonality_method`
+See "report_clonality" for the parameter options.
+
+## Dependencies
+- Linux
+- R
+  - gridExtra
+  - ggplot2
+  - plyr
+  - data.table
+  - reshape2
+  - lymphclon
+
+#### optional
+- Circos
+- IgBlast
+- igblastwrp

diff -r 942eea8359fe -r 4d2a8f98a502 complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml Fri Dec 08 06:32:16 2017 -0500
+++ b/complete_immunerepertoire.xml Mon Jan 28 09:37:41 2019 -0500

@@ -1,4 +1,12 @@
<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.0">
+ <requirements>
+ <requirement type="package" version="2.3">r-gridextra</requirement>
+ <requirement type="package" version="3.0.0">r-ggplot2</requirement>
+ <requirement type="package" version="1.8.4">r-plyr</requirement>
+ <requirement type="package" version="1.11.4">r-data.table</requirement>
+ <requirement type="package" version="1.4.3">r-reshape2</requirement>
+ <requirement type="package" version="1.3.0">r-lymphclon</requirement>
+ </requirements>
<description> </description>
<command interpreter="bash">
complete.sh "

diff -r 942eea8359fe -r 4d2a8f98a502 igblast/igblast.sh
--- a/igblast/igblast.sh Fri Dec 08 06:32:16 2017 -0500
+++ b/igblast/igblast.sh Mon Jan 28 09:37:41 2019 -0500

@@ -24,7 +24,5 @@
echo "$input $species $locus $output"

java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
-#java -Xmx64G -jar $dir/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
-#java -Xmx64G -jar $dir/migmap-1.0.1.jar -p 4 -S "$species" -R $locus ${input} $PWD/blasted_output 2>&1

Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1

diff -r 942eea8359fe -r 4d2a8f98a502 igblastparser/igparse.pl
--- a/igblastparser/igparse.pl Fri Dec 08 06:32:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1252 +0,0 @@\n-#!/usr/bin/perl\n-=head1 IGBLAST_simple.pl\n-\n-This version (1.4) has been heavily adapted since the original program was first created back in October 2012.\n-Bas Horsman (EMC, Rotterdam, The Netherlands) has contributed with minor - though important - code changes.\n-\n-From V 1.2 onwards a \'Change Log\' is included at the end of the program\n-\n-=head2 Usage\n-\n-Requires no modules in general use; the Data::Dumper (supplied as part of the Perl Core module set) might be useful for debugging/adjustment \n-as it allows inspection of the data stores.\n-\n-The program takes a text file of the \n-\n- ./IGBLAST_simple.pl igBLASTOutput.txt <-optional: index of record to process->\n- \n-Supply the text version of the igBLAST report in the format as in the example below.\n-The extra command line arugment is the record number (aka. BLAST report) to process. \n-If 0 or absent all are processed, if supplied that record (base 1) is processed and the program dies afterwards. \n-\n-=head2 Example Input\n-\n-A standard igBLAST record or set of them in a file; this being typical:\n-\n- BLASTN 2.2.27+\n-\n-\n-Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.\n-Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.\n-Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of\n-protein database search programs", Nucleic Acids Res. 25:3389-3402.\n-\n-\n-\n-Database: human_gl_V; human_gl_D; human_gl_J\n- 674 sequences; 179,480 total letters\n-\n-\n-\n-Query= HL67IUI01D26LR length=433 xy=1559_1437 region=1\n-run=R_2012_04_10_11_57_56_\n-\n-Length=433\n- Score E\n-Sequences producing significant alignments: (Bits) Value\n-\n-lcl|IGHV3-30*04 330 2e-92\n-lcl|IGHV3-30-3*01 330 2e-92\n-lcl|IGHV3-30*01 327 2e-91\n-lcl|IGHD3-16*01 14.4 11\n-lcl|IGHD3-16*02 14.4 11\n-lcl|IGHD1-14*01 12.4 43\n-lcl|IGHJ4*02 78.3 1e-18\n-lcl|IGHJ5*02 70.3 4e-16\n-lcl|IGHJ4*01 68.3 2e-15\n-\n-\n-Domain classification requested: imgt\n-\n-\n-V(D)J rearrangement summary for query sequence (Top V gene match, Top D gene match, Top J gene match, Chain type, V-J Frame, Strand):\n-IGHV3-30*04\tIGHD3-16*01\tIGHJ4*02\tVH\tIn-frame\t+\n-\n-V(D)J junction details (V end, V-D junction, D region, D-J junction, J start). Note that possible overlapping nucleotides at VDJ junction (i.e, nucleotides that could be assigned to either joining gene segment) are indicated in parentheses (i.e., (TACT)) but are not included under V, D, or J gene itself\n-AGAGA\tTATGAGCCCCATCATGACA\tACGTTTG\tCCGGAA\tACTAC\t\n-\n-Alignment summary between query and top germline V gene hit (from, to, length, matches, mismatches, gaps, percent identity)\n-FWR1\t27\t38\t12\t11\t1\t0\t91.7\n-CDR1\t39\t62\t24\t22\t2\t0\t91.7\n-FWR2\t63\t113\t51\t50\t1\t0\t98\n-CDR2\t114\t137\t24\t23\t1\t0\t95.8\n-FWR3\t138\t251\t114\t109\t5\t0\t95.6\n-CDR3 (V region only)\t252\t259\t8\t7\t1\t0\t87.5\n-Total\tN/A\tN/A\t233\t222\t11\t0\t95.3\n-\n-\n-Alignments\n-\n- <----FWR1--><----------CDR1--------><-----------------------FWR2------\n- W A A S G F T F N T Y A V H W V R Q A P G K G \n- Query_1 27 TGGGCAGCCTCTGGATTCACCTTCAATACCTATGCTGTGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGC 96\n-V 95.3% (222/233) IGHV3-30*04 64 ..T......................G..G.......A................................. 133\n- C A A S G F T F S S Y A M H W '..b'plit (/\\s+/,$InfoPanel);\t#Split on spaces\n-##Enable if you need to know what we just found: \n-#\t\t#print "D: Fields are (Germclass, PID, PID_Counts, Allele) \\t$Germclass, $PID, $PID_Counts, $Allele\\n";\n-#\t\t#A reality check: we should have an Allele - or some text here.\n-#\t\tunless (defined $Allele && $Allele ne "")\n-#\t\t\t{\twarn "Cannot get Allele for Line \'$C_Line\' - implies improper parsing: \'",substr ($Lines[$C_Line],0,15),"...\'\\n";\t}\n-#\t\tif (exists ($Alginments {$Germclass}{$Allele}))\n-#\t\t\t{\t$Alginments {$Germclass}{$Allele}\t=\t$Alginments {$Germclass}{$Allele}.$CurrentAASequence;\t}\t#Carry on adding\n-#\t\telse\t#more work needed as we need to \'pad\' the sequence with fake gap characters)\n-#\t\t\t{\n-##Do we still need this padding? I don\'t think so\t\t\t\t\n-#\t\t\t\t\n-#\n-#\t\t\tmy $PaddingChars = ($ThisQueryStart-$Query_Start);\n-#\t\t\tprint "D: New gene found: need to pad it with ($ThisQueryStart-$Query_Start) i.e. \'$PaddingChars\' characters\\n";\n-#\t\t\t#To help testing, calculate this first:\n-#\t\t\tmy $PaddingString = " "x $PaddingChars;\n-#\t\t\t$Alginments {$Germclass}{$Allele}\t=\t$CurrentAASequence;\t\n-#\t\t\t}\n-#\t\tnext\n-\n-=head3 Demonstration of Pattern match positions\n-\n-my $Text = "12345TTT TTAAAAA";\n-my $TestPat = "TTT\\\\s+TT";\n-(my $Result)= $Text =~ m/$TestPat/;\n-print "D: Two vars are: - = ",$-[0], " & + =", $+[0]," for test pattern \'$TestPat\'\\n";\n-\n-sub printCDR3 {\n-\n-=head3 Subroutine: printCDR3 ($CDR3_Start, $CDR3_End, "SUMMARY_TABLE", $AAQuerySequence, $DNAQuerySequence);\n-\n-???? IS THIS FUNCTION IN USE ?????\n-\t\n-Handles the printing of the output when passed information about the CDR3 region.\n-\n-\n-The result is sent returned as a text string in this version hence use it like this if you want to send it to STDOUT:\n-\n- print printCDR3 ($CDR3_Start, $CDR3_End, "SUMMARY_TABLE", $AAQuerySequence, $DNAQuerySequence), "\\n";\n- \n-#=cut \t\n-\n-#Despite the similarity in names, these are all local copies passed to us:\n-\n-my ($Start, $End, $Tag, $FullAAQuerySequence, $FullDNAQuerySequence) = @_;\n-\n-#For DNA:\n-my ($CDR_DNA_Seq) = substr ($FullDNAQuerySequence, $Start, $Start+$End);\n-my ($CDR_DNA_Length) = length ($CDR_DNA_Seq);\n-\n-#For AA:\n-my ($CDR_AA_Seq) = substr ($FullAAQuerySequence, $Start, $Start+$End);\n-my ($CDR_AA_Length) = length ($CDR_AA_Seq);\n-\n-my $ReturnString = join ("\\t", $CDR_DNA_Seq, $CDR_DNA_Length, $CDR_AA_Seq, $CDR_AA_Length, $Tag); #Create here so we can inspect it / post process it if needed:\n-print "D: SUB: printCDR3: As returned: \'$ReturnString\'\\n";\n-return ($ReturnString);\n-\n-}\n-\n-=cut \n-\n-\n-\n-=head2 Change Log\n-\n-=head3 Version 1.2\n-\n- 1) Fixed the \'Process recrod request\' feature\' [was failed increment in $Record]\n- 2) Deleted / Deactivated the function \'printCDR3\' [wasn\'t in used; kept if useful for parts]. \n- \tThis function is replaced by the more general printOUTPUTData()\n- 3) A tag for the CDR3 status is now output for every record / read. \n- Initially this is set to "NOT_FOUND" and changed if evidence for the CDR3 is found. \n-\n-=head4 Version 1.3\n-\n- 1) The tophit line was split on whitespace, however sometimes the VJFrame is something like \xe2\x80\x9cIn-frame with stop codon\xe2\x80\x9d, \n- which means the line is also split on the spaces therein. It now splits on tabs only, and this seems to work properly.\n- - found by Bas Horsman. \n-\n-=head4 Version 1.3a\n-\n- 1) "MOTIF_FOUND_IN_AA" reported correctly (was impossible previously due to addition error to the $MotifFound var (never could == 3)\n- \n-=cut \n-\n-=head4 Version 1.4\n-\n- 1) Now processes files using Mac/Unix/MS-DOS newline characters:\n- \n- $_ =~ s/\\r\\n/\\n/g;\t\t#In case line ends are MS-DOS\n- $_ =~ s/\\r/\\n/g;\t\t#In case line ends are Mac\n- #The whole record - one per read - is now stored in $_\n- my @Lines =split (/\\R/,$_);\t#Split on new lines \n-\n-=head4 Version 1.4a\n-\n-1) Fixed the length of the CDR3 AA string being reported correctly:\n-\n- $OUTPUT_Data{"CDR3 Length"} = $CDR3_Length; \n- to: \n- $OUTPUT_Data{"CDR3 Length"} = $CDR3_Seq_AA_Length;\n- \n\\ No newline at end of file\n'

diff -r 942eea8359fe -r 4d2a8f98a502 imgt_loader/imgt_loader.r
--- a/imgt_loader/imgt_loader.r Fri Dec 08 06:32:16 2017 -0500
+++ b/imgt_loader/imgt_loader.r Mon Jan 28 09:37:41 2019 -0500

[

@@ -33,6 +33,16 @@
return(df)
}

+print_missing_columns = function(df, cols, label=""){
+ cols_in_df = cols %in% names(df)
+ if(sum(!cols_in_df) > 0){
+ print("Columns are missing from summary file, don't have:")
+ print(cols[!cols_in_df])
+ } else {
+ print(paste("No missing columns for", label))
+ }
+}
+
summ = fix_column_names(summ)
sequences = fix_column_names(sequences)
aa = fix_column_names(aa)
@@ -51,7 +61,9 @@
added_junction_columns=c('P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION')
added_junction_columns=c(added_junction_columns, 'P5.D1.nt.nb', 'P3.D1.nt.nb', 'N2.REGION.nt.nb', 'P5.D2.nt.nb', 'P3.D2.nt.nb', 'N3.REGION.nt.nb', 'P5.D3.nt.nb', 'P3.D2.nt.nb', 'N4.REGION.nt.nb', 'X5.D1.REGION.trimmed.nt.nb', 'X3.D1.REGION.trimmed.nt.nb', 'X5.D2.REGION.trimmed.nt.nb', 'X3.D2.REGION.trimmed.nt.nb', 'X5.D3.REGION.trimmed.nt.nb', 'X3.D3.REGION.trimmed.nt.nb', 'D.REGION.nt.nb', 'D1.REGION.nt.nb', 'D2.REGION.nt.nb', 'D3.REGION.nt.nb')

-out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")]
+minimum_columns=c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")
+print_missing_columns(summ, minimum_columns)
+out=summ[,minimum_columns]

print(paste("nrow(summ)", nrow(summ)))
print(paste("nrow(aa)", nrow(aa)))

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diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/circos/LTe50048.ttf

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diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/circos/LTe50050.ttf

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diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/circos/LTe50054.ttf

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diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/circos/fonts.conf~
--- a/report_clonality/circos/fonts.conf~ Fri Dec 08 06:32:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-
-default       = LTe50046.ttf
-normal        = LTe50046.ttf
-bold          = LTe50048.ttf
-condensed     = LTe50050.ttf
-condensedbold = LTe50054.ttf
-mono          = pragmata.ttf
-glyph         = wingding.ttf

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/circos/pragmata.ttf

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diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/genes.txt
--- a/report_clonality/genes.txt Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/genes.txt Mon Jan 28 09:37:41 2019 -0500

b'@@ -1,3306 +1,3306 @@\n-Species\tIMGT.GENE.DB\tlocus\tregion\tfunctional\tchr.order\r\n-Bos taurus functional\tTRAJ1\tTRA\tJ\tTRUE\t1\r\n-Bos taurus functional\tTRAJ10\tTRA\tJ\tTRUE\t2\r\n-Bos taurus functional\tTRAJ11\tTRA\tJ\tTRUE\t3\r\n-Bos taurus non-functional\tTRAJ12\tTRA\tJ\tFALSE\t4\r\n-Bos taurus functional\tTRAJ13\tTRA\tJ\tTRUE\t5\r\n-Bos taurus functional\tTRAJ14\tTRA\tJ\tTRUE\t6\r\n-Bos taurus functional\tTRAJ15\tTRA\tJ\tTRUE\t7\r\n-Bos taurus functional\tTRAJ16\tTRA\tJ\tTRUE\t8\r\n-Bos taurus functional\tTRAJ17\tTRA\tJ\tTRUE\t9\r\n-Bos taurus functional\tTRAJ18\tTRA\tJ\tTRUE\t10\r\n-Bos taurus functional\tTRAJ19\tTRA\tJ\tTRUE\t11\r\n-Bos taurus functional\tTRAJ2\tTRA\tJ\tTRUE\t12\r\n-Bos taurus functional\tTRAJ20\tTRA\tJ\tTRUE\t13\r\n-Bos taurus functional\tTRAJ21\tTRA\tJ\tTRUE\t14\r\n-Bos taurus functional\tTRAJ22\tTRA\tJ\tTRUE\t15\r\n-Bos taurus functional\tTRAJ23\tTRA\tJ\tTRUE\t16\r\n-Bos taurus functional\tTRAJ24\tTRA\tJ\tTRUE\t17\r\n-Bos taurus functional\tTRAJ25\tTRA\tJ\tTRUE\t18\r\n-Bos taurus functional\tTRAJ26\tTRA\tJ\tTRUE\t19\r\n-Bos taurus non-functional\tTRAJ27\tTRA\tJ\tFALSE\t20\r\n-Bos taurus functional\tTRAJ28\tTRA\tJ\tTRUE\t21\r\n-Bos taurus functional\tTRAJ29\tTRA\tJ\tTRUE\t22\r\n-Bos taurus functional\tTRAJ3\tTRA\tJ\tTRUE\t23\r\n-Bos taurus non-functional\tTRAJ30\tTRA\tJ\tFALSE\t24\r\n-Bos taurus functional\tTRAJ31\tTRA\tJ\tTRUE\t25\r\n-Bos taurus functional\tTRAJ32\tTRA\tJ\tTRUE\t26\r\n-Bos taurus functional\tTRAJ33\tTRA\tJ\tTRUE\t27\r\n-Bos taurus functional\tTRAJ34\tTRA\tJ\tTRUE\t28\r\n-Bos taurus functional\tTRAJ35\tTRA\tJ\tTRUE\t29\r\n-Bos taurus functional\tTRAJ36\tTRA\tJ\tTRUE\t30\r\n-Bos taurus functional\tTRAJ37\tTRA\tJ\tTRUE\t31\r\n-Bos taurus functional\tTRAJ38\tTRA\tJ\tTRUE\t32\r\n-Bos taurus functional\tTRAJ39\tTRA\tJ\tTRUE\t33\r\n-Bos taurus non-functional\tTRAJ4\tTRA\tJ\tFALSE\t34\r\n-Bos taurus functional\tTRAJ40\tTRA\tJ\tTRUE\t35\r\n-Bos taurus functional\tTRAJ41\tTRA\tJ\tTRUE\t36\r\n-Bos taurus functional\tTRAJ42\tTRA\tJ\tTRUE\t37\r\n-Bos taurus functional\tTRAJ43\tTRA\tJ\tTRUE\t38\r\n-Bos taurus functional\tTRAJ44\tTRA\tJ\tTRUE\t39\r\n-Bos taurus functional\tTRAJ45\tTRA\tJ\tTRUE\t40\r\n-Bos taurus functional\tTRAJ46\tTRA\tJ\tTRUE\t41\r\n-Bos taurus non-functional\tTRAJ47\tTRA\tJ\tFALSE\t42\r\n-Bos taurus functional\tTRAJ48\tTRA\tJ\tTRUE\t43\r\n-Bos taurus functional\tTRAJ49\tTRA\tJ\tTRUE\t44\r\n-Bos taurus functional\tTRAJ5\tTRA\tJ\tTRUE\t45\r\n-Bos taurus functional\tTRAJ50\tTRA\tJ\tTRUE\t46\r\n-Bos taurus functional\tTRAJ51\tTRA\tJ\tTRUE\t47\r\n-Bos taurus non-functional\tTRAJ52\tTRA\tJ\tFALSE\t48\r\n-Bos taurus functional\tTRAJ6\tTRA\tJ\tTRUE\t49\r\n-Bos taurus functional\tTRAJ7\tTRA\tJ\tTRUE\t50\r\n-Bos taurus functional\tTRAJ8\tTRA\tJ\tTRUE\t51\r\n-Bos taurus functional\tTRAJ9\tTRA\tJ\tTRUE\t52\r\n-Bos taurus functional\tTRDD1\tTRD\tD\tTRUE\t53\r\n-Bos taurus functional\tTRDD2\tTRD\tD\tTRUE\t54\r\n-Bos taurus functional\tTRDD3\tTRD\tD\tTRUE\t55\r\n-Bos taurus functional\tTRDD4\tTRD\tD\tTRUE\t56\r\n-Bos taurus functional\tTRDD5\tTRD\tD\tTRUE\t57\r\n-Bos taurus functional\tTRDJ1\tTRD\tJ\tTRUE\t58\r\n-Bos taurus functional\tTRDJ2\tTRD\tJ\tTRUE\t59\r\n-Bos taurus functional\tTRDJ3\tTRD\tJ\tTRUE\t60\r\n-Bos taurus functional\tTRDV1S1\tTRD\tV\tTRUE\t61\r\n-Bos taurus functional\tTRDV1S10\tTRD\tV\tTRUE\t62\r\n-Bos taurus functional\tTRDV1S11\tTRD\tV\tTRUE\t63\r\n-Bos taurus functional\tTRDV1S12\tTRD\tV\tTRUE\t64\r\n-Bos taurus functional\tTRDV1S13-1\tTRD\tV\tTRUE\t65\r\n-Bos taurus functional\tTRDV1S13-2\tTRD\tV\tTRUE\t66\r\n-Bos taurus functional\tTRDV1S14\tTRD\tV\tTRUE\t67\r\n-Bos taurus functional\tTRDV1S15-1\tTRD\tV\tTRUE\t68\r\n-Bos taurus functional\tTRDV1S15-2\tTRD\tV\tTRUE\t69\r\n-Bos taurus functional\tTRDV1S16\tTRD\tV\tTRUE\t70\r\n-Bos taurus functional\tTRDV1S17\tTRD\tV\tTRUE\t71\r\n-Bos taurus functional\tTRDV1S18-1\tTRD\tV\tTRUE\t72\r\n-Bos taurus functional\tTRDV1S18-2\tTRD\tV\tTRUE\t73\r\n-Bos taurus functional\tTRDV1S19\tTRD\tV\tTRUE\t74\r\n-Bos taurus non-functional\tTRDV1S2-1\tTRD\tV\tFALSE\t75\r\n-Bos taurus non-functional\tTRDV1S2-2\tTRD\tV\tFALSE\t76\r\n-Bos taurus functional\tTRDV1S20\tTRD\tV\tTRUE\t77\r\n-Bos taurus functional\tTRDV1S21-1\tTRD\tV\tTRUE\t78\r\n-Bos taurus functional\tTRDV1S21-2\tTRD\tV\tTRUE\t79\r\n-Bos taurus non-functional\tTRDV1S22\tTRD\tV\tFALSE\t80\r\n-Bos taurus functional\tTRDV1S23\tTRD\tV\tTRUE\t81\r\n-Bos taurus functional\tTRDV1S24\tTRD\tV\tTRUE\t82\r\n-Bos taurus non-functional\tTRDV1S25-1\tTRD\tV\tFALSE\t83\r\n-Bos taurus non-functional\tTRDV1S25-2\tTRD\tV\tFALSE\t84\r\n-Bos taurus functional\tTRDV1S26\tTRD\tV\tTRUE'..b's functional\tIGLV1S1\tIGL\tV\tTRUE\t3224\n+Rattus norvegicus functional\tIGLV2S1\tIGL\tV\tTRUE\t3225\n+Rattus norvegicus functional\tIGLV3S1\tIGL\tV\tTRUE\t3226\n+Rattus norvegicus functional\tIGLV3S2\tIGL\tV\tTRUE\t3227\n+Rattus norvegicus functional\tIGLV3S3\tIGL\tV\tTRUE\t3228\n+Rattus norvegicus functional\tIGLV3S4\tIGL\tV\tTRUE\t3229\n+Rattus norvegicus functional\tIGLV3S5\tIGL\tV\tTRUE\t3230\n+Sus scrofa functional\tIGHD\tIGH\tD\tTRUE\t3231\n+Sus scrofa functional\tIGHD1\tIGH\tD\tTRUE\t3232\n+Sus scrofa functional\tIGHD2\tIGH\tD\tTRUE\t3233\n+Sus scrofa functional\tIGHD3\tIGH\tD\tTRUE\t3234\n+Sus scrofa functional\tIGHD4\tIGH\tD\tTRUE\t3235\n+Sus scrofa functional\tIGHJ1\tIGH\tJ\tTRUE\t3236\n+Sus scrofa functional\tIGHJ2\tIGH\tJ\tTRUE\t3237\n+Sus scrofa functional\tIGHJ3\tIGH\tJ\tTRUE\t3238\n+Sus scrofa functional\tIGHJ4\tIGH\tJ\tTRUE\t3239\n+Sus scrofa functional\tIGHJ5\tIGH\tJ\tTRUE\t3240\n+Sus scrofa non-functional\tIGHV1-1\tIGH\tV\tFALSE\t3241\n+Sus scrofa functional\tIGHV1-10\tIGH\tV\tTRUE\t3242\n+Sus scrofa functional\tIGHV1-11\tIGH\tV\tTRUE\t3243\n+Sus scrofa functional\tIGHV1-12\tIGH\tV\tTRUE\t3244\n+Sus scrofa non-functional\tIGHV1-13\tIGH\tV\tFALSE\t3245\n+Sus scrofa functional\tIGHV1-14\tIGH\tV\tTRUE\t3246\n+Sus scrofa functional\tIGHV1-15\tIGH\tV\tTRUE\t3247\n+Sus scrofa functional\tIGHV1-2\tIGH\tV\tTRUE\t3248\n+Sus scrofa non-functional\tIGHV1-3\tIGH\tV\tFALSE\t3249\n+Sus scrofa functional\tIGHV1-4\tIGH\tV\tTRUE\t3250\n+Sus scrofa functional\tIGHV1-5\tIGH\tV\tTRUE\t3251\n+Sus scrofa functional\tIGHV1-6\tIGH\tV\tTRUE\t3252\n+Sus scrofa non-functional\tIGHV1-7\tIGH\tV\tFALSE\t3253\n+Sus scrofa functional\tIGHV1-8\tIGH\tV\tTRUE\t3254\n+Sus scrofa non-functional\tIGHV1-9\tIGH\tV\tFALSE\t3255\n+Sus scrofa functional\tIGHV1S2\tIGH\tV\tTRUE\t3256\n+Sus scrofa non-functional\tIGHV1S3\tIGH\tV\tFALSE\t3257\n+Sus scrofa functional\tIGHV1S5\tIGH\tV\tTRUE\t3258\n+Sus scrofa functional\tIGHV1S6\tIGH\tV\tTRUE\t3259\n+Sus scrofa non-functional\tIGHV1S7\tIGH\tV\tFALSE\t3260\n+Sus scrofa non-functional\tIGHV1S8\tIGH\tV\tFALSE\t3261\n+Sus scrofa functional\tIGKJ1\tIGK\tJ\tTRUE\t3262\n+Sus scrofa functional\tIGKJ2\tIGK\tJ\tTRUE\t3263\n+Sus scrofa functional\tIGKJ3\tIGK\tJ\tTRUE\t3264\n+Sus scrofa functional\tIGKJ4\tIGK\tJ\tTRUE\t3265\n+Sus scrofa functional\tIGKJ5\tIGK\tJ\tTRUE\t3266\n+Sus scrofa functional\tIGKV1-11\tIGK\tV\tTRUE\t3267\n+Sus scrofa functional\tIGKV1-14\tIGK\tV\tTRUE\t3268\n+Sus scrofa functional\tIGKV1-7\tIGK\tV\tTRUE\t3269\n+Sus scrofa functional\tIGKV1-9\tIGK\tV\tTRUE\t3270\n+Sus scrofa functional\tIGKV1D-11\tIGK\tV\tTRUE\t3271\n+Sus scrofa functional\tIGKV2-10\tIGK\tV\tTRUE\t3272\n+Sus scrofa functional\tIGKV2-12\tIGK\tV\tTRUE\t3273\n+Sus scrofa functional\tIGKV2-13\tIGK\tV\tTRUE\t3274\n+Sus scrofa non-functional\tIGKV2-5\tIGK\tV\tFALSE\t3275\n+Sus scrofa functional\tIGKV2-6\tIGK\tV\tTRUE\t3276\n+Sus scrofa functional\tIGKV2-8\tIGK\tV\tTRUE\t3277\n+Sus scrofa non-functional\tIGKV2/OR3-1\tIGK\tV\tFALSE\t3278\n+Sus scrofa functional\tIGKV2D-12\tIGK\tV\tTRUE\t3279\n+Sus scrofa non-functional\tIGKV3-3\tIGK\tV\tFALSE\t3280\n+Sus scrofa non-functional\tIGKV5-4\tIGK\tV\tFALSE\t3281\n+Sus scrofa functional\tIGLJ2\tIGL\tJ\tTRUE\t3282\n+Sus scrofa functional\tIGLJ3\tIGL\tJ\tTRUE\t3283\n+Sus scrofa functional\tIGLJ4\tIGL\tJ\tTRUE\t3284\n+Sus scrofa non-functional\tIGLV(III)-8\tIGL\tV\tFALSE\t3285\n+Sus scrofa non-functional\tIGLV1-15\tIGL\tV\tFALSE\t3286\n+Sus scrofa non-functional\tIGLV1-20\tIGL\tV\tFALSE\t3287\n+Sus scrofa functional\tIGLV2-6\tIGL\tV\tTRUE\t3288\n+Sus scrofa non-functional\tIGLV3-1\tIGL\tV\tFALSE\t3289\n+Sus scrofa functional\tIGLV3-2\tIGL\tV\tTRUE\t3290\n+Sus scrofa functional\tIGLV3-3\tIGL\tV\tTRUE\t3291\n+Sus scrofa functional\tIGLV3-4\tIGL\tV\tTRUE\t3292\n+Sus scrofa functional\tIGLV3-5\tIGL\tV\tTRUE\t3293\n+Sus scrofa non-functional\tIGLV5-11\tIGL\tV\tFALSE\t3294\n+Sus scrofa functional\tIGLV5-14\tIGL\tV\tTRUE\t3295\n+Sus scrofa non-functional\tIGLV5-17\tIGL\tV\tFALSE\t3296\n+Sus scrofa non-functional\tIGLV5-22\tIGL\tV\tFALSE\t3297\n+Sus scrofa non-functional\tIGLV7-7\tIGL\tV\tFALSE\t3298\n+Sus scrofa non-functional\tIGLV7-9\tIGL\tV\tFALSE\t3299\n+Sus scrofa functional\tIGLV8-10\tIGL\tV\tTRUE\t3300\n+Sus scrofa functional\tIGLV8-13\tIGL\tV\tTRUE\t3301\n+Sus scrofa non-functional\tIGLV8-16\tIGL\tV\tFALSE\t3302\n+Sus scrofa functional\tIGLV8-18\tIGL\tV\tTRUE\t3303\n+Sus scrofa functional\tIGLV8-19\tIGL\tV\tTRUE\t3304\n+Sus scrofa non-functional\tIGLV8-21\tIGL\tV\tFALSE\t3305\n'

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_cdr3_char.htm
--- a/report_clonality/naive_cdr3_char.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_cdr3_char.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,101 +1,101 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-CDR3 characteristics tab
-
-This tab gives information on the
-different characteristics of the CDR3.
-
-Graphs
-
-length distribution of CDR3
-
-Graph visualizing for each donor the
-distribution of the CDR3 length in amino acids between all sequences.
-
-Amino acid composition of CDR3
-
-Bar graph visualizing for each donor how
-frequent each amino acid is used in the CDR3 of all sequences. The red colour
-in the background indicate positively charged amino acids, and the blue colour
-in the background indicate negatively charged amino acids. The amino acids are
-ordered from hydrophilic (left) to hydrophobic (right). 
-
-Table
-
-Table showing for each donor the median
-CDR3 length.
-
- 
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+CDR3 characteristics tab
+
+This tab gives information on the
+different characteristics of the CDR3.
+
+Graphs
+
+length distribution of CDR3
+
+Graph visualizing for each donor the
+distribution of the CDR3 length in amino acids between all sequences.
+
+Amino acid composition of CDR3
+
+Bar graph visualizing for each donor how
+frequent each amino acid is used in the CDR3 of all sequences. The red colour
+in the background indicate positively charged amino acids, and the blue colour
+in the background indicate negatively charged amino acids. The amino acids are
+ordered from hydrophilic (left) to hydrophobic (right). 
+
+Table
+
+Table showing for each donor the median
+CDR3 length.
+
+ 
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_circos.htm
--- a/report_clonality/naive_circos.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_circos.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,59 +1,59 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-Martin Krzywinski, Jacqueline Schein, İnan�
-Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco
-A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome
-Research 10.1101/gr.092759.109.
-
-Circos plot showing the V-D, V-J, and D-J gen usage.
-The thicker the line the more frequent this gene combination is used.
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+Martin Krzywinski, Jacqueline Schein, İnan�
+Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco
+A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome
+Research 10.1101/gr.092759.109.
+
+Circos plot showing the V-D, V-J, and D-J gen usage.
+The thicker the line the more frequent this gene combination is used.
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_clonality.htm
--- a/report_clonality/naive_clonality.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_clonality.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,67 +1,67 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-For each donor a
-subtab is provided containing information on the sequence overlap between
-replicates of the different replicates of one donor. Dependent on the settings
-of the Shared clonal types / clonality filter a clonality score is given.� The clonality
-score �is calculated according to the formula described by <a
-name="OLE_LINK13"></a><a name="OLE_LINK12"></a><a name="OLE_LINK11">Boyd
-et al, PMID: 20161664. </a>
-
-For each
-individual replicate the number of reads is reported. In addition, the number
-of coincidences between the different replicates of the same donor are reported.
-
-
- 
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+For each donor a
+subtab is provided containing information on the sequence overlap between
+replicates of the different replicates of one donor. Dependent on the settings
+of the Shared clonal types / clonality filter a clonality score is given.� The clonality
+score �is calculated according to the formula described by <a
+name="OLE_LINK13"></a><a name="OLE_LINK12"></a><a name="OLE_LINK11">Boyd
+et al, PMID: 20161664. </a>
+
+For each
+individual replicate the number of reads is reported. In addition, the number
+of coincidences between the different replicates of the same donor are reported.
+
+
+ 
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_compare.htm
--- a/report_clonality/naive_compare.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_compare.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,61 +1,61 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-The tab allows
-you to compare the VD, VJ and DJ heatmaps of multiple donors to each other. 
-
-By ticking the include box of a donor, the three
-heatmaps of this donor is visualized underneath eachother. By clicking the
-include box of multiple replicates the heatmaps of these replicates are visualized
-next to each other allowing easy comparison of heatmaps. 
-
- 
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+The tab allows
+you to compare the VD, VJ and DJ heatmaps of multiple donors to each other. 
+
+By ticking the include box of a donor, the three
+heatmaps of this donor is visualized underneath eachother. By clicking the
+include box of multiple replicates the heatmaps of these replicates are visualized
+next to each other allowing easy comparison of heatmaps. 
+
+ 
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_downloads.htm
--- a/report_clonality/naive_downloads.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_downloads.htm Mon Jan 28 09:37:41 2019 -0500

b'@@ -1,197 +1,197 @@\n-<html>\r\n-\r\n-<head>\r\n-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">\r\n-<meta name=Generator content="Microsoft Word 14 (filtered)">\r\n-<style>\r\n-\r\n-</style>\r\n-\r\n-</head>\r\n-\r\n-<body lang=EN-US>\r\n-\r\n-<div class=WordSection1>\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Downloads\r\n-tab\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Description\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\r\n-filtered dataset: <a name="OLE_LINK15"></a><a\r\n-name="OLE_LINK14">Allows you to download information on V D and J gene usage,\r\n-the junctions and the amino acid sequence of the sequences that passed the chosen\r\n-filter settings. Note: this file contains only 1 sequences of a replicate\r\n-sequence. </a>\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Gene\r\n-frequencies\r\n-\r\n-The dataset used to generate the distribution\r\n-of V gene families graph: Downloads a table with information used to generate\r\n-the distribution of V gene families graph.\r\n-\r\n-The dataset used to generate\xa0 the\r\n-distribution of D gene families graph: Downloads a table with information used\r\n-to generate the distribution of D gene families graph.\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\r\n-dataset used to generate the relative frequency of V gene usage graph:<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\r\n-Downloads the data used to generate the relative frequency of V gene usage\r\n-graph. In addition information on the chromosomal order of the V genes can be\r\n-found.\r\n-\r\n-<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\r\n-dataset used to generate the relative frequency of D gene usage graph:<span\r\n-style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\r\n-Downloads the data used to generate the relative frequency of D gene usage\r\n-graph. In addition information on the chromosomal order of the D genes can be\r\n-found. \r\n-\r\n-<'..b'the VD heatmap for \x93donor name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the VD heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+data used to generate the VJ heatmap for \x93donor name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the VJ heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+data used to generate the DJ heatmap for \x93sample name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the DJ heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Circos\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+data used to generate the VD circus plots for \x93donor name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the VD heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+data used to generate the VJ circus plots for \x93donor name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the VJ heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+data used to generate the DJ circus plots for \x93sample name\x94:<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+Downloads the data set used for the generation of the DJ heatmap. For each\n+uploaded donor a separate download is generated.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Clonality\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>The\n+dataset used to calculate clonality score: Allows you to\n+download information on V D and J gene usage, the junctions and the amino acid\n+sequence of the sequences that passed the chosen filter settings. Note: this\n+file contains all the replicate sequences form the different input files.\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Sequences\n+that are present in more than one replicate: Allows you to\n+download a table containing all the sequences that were present in more than\n+one replicate. It provides the concidence type, clonaltype, sequence name,\n+replicate number, and the nucleotide sequence\n+\n+ \n+\n+</div>\n+\n+</body>\n+\n+</html>\n'

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_gene_freq.htm
--- a/report_clonality/naive_gene_freq.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_gene_freq.htm Mon Jan 28 09:37:41 2019 -0500

[

b'@@ -1,220 +1,220 @@\n-<html xmlns:v="urn:schemas-microsoft-com:vml"\r\n-xmlns:o="urn:schemas-microsoft-com:office:office"\r\n-xmlns:w="urn:schemas-microsoft-com:office:word"\r\n-xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"\r\n-xmlns="http://www.w3.org/TR/REC-html40">\r\n-\r\n-<head>\r\n-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">\r\n-<meta name=ProgId content=Word.Document>\r\n-<meta name=Generator content="Microsoft Word 14">\r\n-<meta name=Originator content="Microsoft Word 14">\r\n-<link rel=File-List href="Gene%20frequencies%20tab_files/filelist.xml">\r\n-<link rel=themeData href="Gene%20frequencies%20tab_files/themedata.thmx">\r\n-<style>\r\n-\r\n-</style>\r\n-\r\n-</head>\r\n-\r\n-<body lang=EN-US style=\'tab-interval'..b'-height:normal\'>Distribution of\n+V gene families<o:p></o:p>\n+\n+<a name="OLE_LINK121"></a><a\n+name="OLE_LINK123"></a><a name="OLE_LINK122"></a>Bar graph showing the frequency of V gene family usage\n+in all uploaded donors. <o:p></o:p>\n+\n+<o:p> </o:p>\n+\n+Relative\n+frequency of V gene usage<o:p></o:p>\n+\n+<a name="OLE_LINK124"></a><a\n+name="OLE_LINK126"></a><a name="OLE_LINK125"></a>Bar graph showing the frequency of V genes in all\n+uploaded donors. The order of the V genes on the x-axis can be altered by\n+altering the \x93Order of V(D)J genes\n+in graphs\x94 filter on the main page of the Immune repertoire pipeline.<span\n+lang=EN-GB style=\'font-size:12.0pt;font-family:"Times New Roman","serif";\n+color:black;background:white;mso-ansi-language:EN-GB\'><o:p></o:p>\n+\n+<o:p> </o:p>\n+\n+Relative\n+frequency of D gene usage<o:p></o:p>\n+\n+Bar graph showing the frequency of D genes in all uploaded donors. The\n+order of the D genes on the x-axis can be altered by altering the \x93<span\n+style=\'color:black;background:white\'>Order of V(D)J genes in graphs\x94 filter on\n+the main page of the Immune repertoire pipeline.<o:p></o:p>\n+\n+<o:p> </o:p>\n+\n+Relative\n+frequency of J gene usage<o:p></o:p>\n+\n+Bar graph showing the frequency of J genes in all uploaded donors. The\n+order of the J genes on the x-axis can be altered by altering the \x93<span\n+style=\'color:black;background:white\'>Order of V(D)J genes in graphs\x94 filter on\n+the main page of the Immune repertoire pipeline.<o:p></o:p>\n+\n+<o:p> </o:p>\n+\n+D\n+reading frame<o:p></o:p>\n+\n+Bar graph visualizing the frequency by which each D reading frame is\n+used in each donor.\n+\n+</div>\n+\n+</body>\n+\n+</html>\n'

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_heatmap.htm
--- a/report_clonality/naive_heatmap.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_heatmap.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,57 +1,57 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-In this tab
-heatmaps are provided showing the frequency of different combinations V and D,
-D and J and V and J genes according together. For each donor a subtab with all
-three heatmaps is provided.
-
- 
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+In this tab
+heatmaps are provided showing the frequency of different combinations V and D,
+D and J and V and J genes according together. For each donor a subtab with all
+three heatmaps is provided.
+
+ 
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_junction.htm
--- a/report_clonality/naive_junction.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_junction.htm Mon Jan 28 09:37:41 2019 -0500

[

b'@@ -1,206 +1,206 @@\n-<html xmlns:v="urn:schemas-microsoft-com:vml"\r\n-xmlns:o="urn:schemas-microsoft-com:office:office"\r\n-xmlns:w="urn:schemas-microsoft-com:office:word"\r\n-xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"\r\n-xmlns="http://www.w3.org/TR/REC-html40">\r\n-\r\n-<head>\r\n-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">\r\n-<meta name=ProgId content=Word.Document>\r\n-<meta name=Generator content="Microsoft Word 14">\r\n-<meta name=Originator content="Microsoft Word 14">\r\n-<link rel=File-List href="Junction%20analysis%20tab_files/filelist.xml">\r\n-<link rel=themeData href="Junction%20analysis%20tab_files/themedata.thmx">\r\n-<style>\r\n-\r\n-</style>\r\n-\n+</head>\n+\n+<body lang=EN-US style=\'tab-interval:.5in\'>\n+\n+<div class=WordSection1>\n+\n+Junction\n+analysis tab \n+\n+Tables:\n+\n+The unique\n+rearrangements are separated in sequences that contain both a\n+V, D and J gene and sequences that contain only a V and J gene.\n+\n+Productive mean\n+tables<o:p></o:p>\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Reports\n+for each donor the number of productive sequences and the mean number of\n+deletions, N-nucleotides and P-nucleotides.<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+For explanation about the different deletions and N and P nucleotides see\n+figure above. \n+\n+Unproductive\n+mean table<o:p></o:p>\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Reports\n+for each donor the number of unproductive sequences and the mean number of\n+deletions, N-nucleotides and P-nucleotides.<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+For explanation about the different deletions and N and P nucleotides see\n+figure above. \n+\n+Productive\n+median table<o:p></o:p>\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Reports\n+for each donor the number of productive sequences and the median number of\n+deletions, N-nucleotides and P-nucleotides.<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+For explanation about the different deletions and N and P nucleotides see\n+figure above. \n+\n+Unproductive\n+median table<o:p></o:p>\n+\n+<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>Reports\n+for each donor the number of unproductive sequences and the median number of\n+deletions, N-nucleotides and P-nucleotides.<span\n+style=\'font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"\'>\n+For explanation about the different deletions and N and P nucleotides see\n+figure above. \n+\n+ \n+\n+</div>\n+\n+</body>\n+\n+</html>\n'

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/naive_overview.htm
--- a/report_clonality/naive_overview.htm Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/naive_overview.htm Mon Jan 28 09:37:41 2019 -0500

@@ -1,65 +1,65 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-
-</style>
-
-</head>
-
-<body lang=EN-US>
-
-<div class=WordSection1>
-
-Table showing the number and percentage of
-(unique) productive and unproductive sequences per sample and per replicate. 
-
- 
-
-The definition
-of unique sequences is based on the clonal type definition filter setting
-chosen.
-
- 
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+
+</style>
+
+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+Table showing the number and percentage of
+(unique) productive and unproductive sequences per sample and per replicate. 
+
+ 
+
+The definition
+of unique sequences is based on the clonal type definition filter setting
+chosen.
+
+ 
+
+</div>
+
+</body>
+
+</html>

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/style.css
--- a/report_clonality/style.css Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/style.css Mon Jan 28 09:37:41 2019 -0500

@@ -1,109 +1,109 @@
-/* $Id: example.css,v 1.5 2006/03/27 02:44:36 pat Exp $ */
-
-/*--------------------------------------------------
-  REQUIRED to hide the non-active tab content.
-  But do not hide them in the print stylesheet!
-  --------------------------------------------------*/
-.tabberlive .tabbertabhide {
- display:none;
-}
-
-/*--------------------------------------------------
-  .tabber = before the tabber interface is set up
-  .tabberlive = after the tabber interface is set up
-  --------------------------------------------------*/
-.tabber {
-}
-.tabberlive {
- margin-top:1em;
-}
-
-/*--------------------------------------------------
-  ul.tabbernav = the tab navigation list
-  li.tabberactive = the active tab
-  --------------------------------------------------*/
-ul.tabbernav
-{
- margin:0;
- padding: 3px 0;
- border-bottom: 1px solid #778;
- font: bold 12px Verdana, sans-serif;
-}
-
-ul.tabbernav li
-{
- list-style: none;
- margin: 0;
- display: inline;
-}
-
-ul.tabbernav li a
-{
- padding: 3px 0.5em;
- margin-left: 3px;
- border: 1px solid #778;
- border-bottom: none;
- background: #DDE;
- text-decoration: none;
-}
-
-ul.tabbernav li a:link { color: #448; }
-ul.tabbernav li a:visited { color: #667; }
-
-ul.tabbernav li a:hover
-{
- color: #000;
- background: #AAE;
- border-color: #227;
-}
-
-ul.tabbernav li.tabberactive a
-{
- background-color: #fff;
- border-bottom: 1px solid #fff;
-}
-
-ul.tabbernav li.tabberactive a:hover
-{
- color: #000;
- background: white;
- border-bottom: 1px solid white;
-}
-
-/*--------------------------------------------------
-  .tabbertab = the tab content
-  Add style only after the tabber interface is set up (.tabberlive)
-  --------------------------------------------------*/
-.tabberlive .tabbertab {
- padding:5px;
- border:1px solid #aaa;
- border-top:0;
-
- /* If you don't want the tab size changing whenever a tab is changed
-    you can set a fixed height */
-
- /* height:200px; */
-
- /* If you set a fix height set overflow to auto and you will get a
-    scrollbar when necessary */
-
- /* overflow:auto; */
-}
-
-/* If desired, hide the heading since a heading is provided by the tab */
-.tabberlive .tabbertab h2 {
- display:none;
-}
-.tabberlive .tabbertab h3 {
- display:none;
-}
-
-/* Example of using an ID to set different styles for the tabs on the page */
-.tabberlive#tab1 {
-}
-.tabberlive#tab2 {
-}
-.tabberlive#tab2 .tabbertab {
- height:200px;
- overflow:auto;
-}
+/* $Id: example.css,v 1.5 2006/03/27 02:44:36 pat Exp $ */
+
+/*--------------------------------------------------
+  REQUIRED to hide the non-active tab content.
+  But do not hide them in the print stylesheet!
+  --------------------------------------------------*/
+.tabberlive .tabbertabhide {
+ display:none;
+}
+
+/*--------------------------------------------------
+  .tabber = before the tabber interface is set up
+  .tabberlive = after the tabber interface is set up
+  --------------------------------------------------*/
+.tabber {
+}
+.tabberlive {
+ margin-top:1em;
+}
+
+/*--------------------------------------------------
+  ul.tabbernav = the tab navigation list
+  li.tabberactive = the active tab
+  --------------------------------------------------*/
+ul.tabbernav
+{
+ margin:0;
+ padding: 3px 0;
+ border-bottom: 1px solid #778;
+ font: bold 12px Verdana, sans-serif;
+}
+
+ul.tabbernav li
+{
+ list-style: none;
+ margin: 0;
+ display: inline;
+}
+
+ul.tabbernav li a
+{
+ padding: 3px 0.5em;
+ margin-left: 3px;
+ border: 1px solid #778;
+ border-bottom: none;
+ background: #DDE;
+ text-decoration: none;
+}
+
+ul.tabbernav li a:link { color: #448; }
+ul.tabbernav li a:visited { color: #667; }
+
+ul.tabbernav li a:hover
+{
+ color: #000;
+ background: #AAE;
+ border-color: #227;
+}
+
+ul.tabbernav li.tabberactive a
+{
+ background-color: #fff;
+ border-bottom: 1px solid #fff;
+}
+
+ul.tabbernav li.tabberactive a:hover
+{
+ color: #000;
+ background: white;
+ border-bottom: 1px solid white;
+}
+
+/*--------------------------------------------------
+  .tabbertab = the tab content
+  Add style only after the tabber interface is set up (.tabberlive)
+  --------------------------------------------------*/
+.tabberlive .tabbertab {
+ padding:5px;
+ border:1px solid #aaa;
+ border-top:0;
+
+ /* If you don't want the tab size changing whenever a tab is changed
+    you can set a fixed height */
+
+ /* height:200px; */
+
+ /* If you set a fix height set overflow to auto and you will get a
+    scrollbar when necessary */
+
+ /* overflow:auto; */
+}
+
+/* If desired, hide the heading since a heading is provided by the tab */
+.tabberlive .tabbertab h2 {
+ display:none;
+}
+.tabberlive .tabbertab h3 {
+ display:none;
+}
+
+/* Example of using an ID to set different styles for the tabs on the page */
+.tabberlive#tab1 {
+}
+.tabberlive#tab2 {
+}
+.tabberlive#tab2 .tabbertab {
+ height:200px;
+ overflow:auto;
+}

diff -r 942eea8359fe -r 4d2a8f98a502 report_clonality/tabber.js
--- a/report_clonality/tabber.js Fri Dec 08 06:32:16 2017 -0500
+++ b/report_clonality/tabber.js Mon Jan 28 09:37:41 2019 -0500

[

b'@@ -1,40 +1,40 @@\n-/* Copyright (c) 2006 Patrick Fitzgerald */\r\n-\r\n-function tabberObj(argsObj)\r\n-{var arg;this.div=null;this.classMain="tabber";this.classMainLive="tabberlive";this.classTab="tabbertab";this.classTabDefault="tabbertabdefault";this.classNav="tabbernav";this.classTabHide="tabbertabhide";this.classNavActive="tabberactive";this.titleElements=[\'h2\',\'h3\',\'h4\',\'h5\',\'h6\'];this.titleElementsStripHTML=true;this.removeTitle=true;this.addLinkId=false;this.linkIdFormat=\'<tabberid>nav<tabnumberone>\';for(arg in argsObj){this[arg]=argsObj[arg];}\r\n-this.REclassMain=new RegExp(\'\\\\b\'+this.classMain+\'\\\\b\',\'gi\');this.REclassMainLive=new RegExp(\'\\\\b\'+this.classMainLive+\'\\\\b\',\'gi\');this.REclassTab=new RegExp(\'\\\\b\'+this.classTab+\'\\\\b\',\'gi\');this.REclassTabDefault=new RegExp(\'\\\\b\'+this.classTabDefault+\'\\\\b\',\'gi\');this.REclassTabHide=new RegExp(\'\\\\b\'+this.classTabHide+\'\\\\b\',\'gi\');this.tabs=new Array();if(this.div){this.init(this.div);this.div=null;}}\r\n-tabberObj.prototype.init=function(e)\r\n-{var\r\n-childNodes,i,i2,t,defaultTab=0,DOM_ul,DOM_li,DOM_a,aId,headingElement;if(!document.getElementsByTagName){return false;}\r\n-if(e.id){this.id=e.id;}\r\n-this.tabs.length=0;childNodes=e.childNodes;for(i=0;i<childNodes.length;i++){if(childNodes[i].className&&childNodes[i].className.match(this.REclassTab)){t=new Object();t.div=childNodes[i];this.tabs[this.tabs.length]=t;if(childNodes[i].className.match(this.REclassTabDefault)){defaultTab=this.tabs.length-1;}}}\r\n-DOM_ul=document.createElement("ul");DOM_ul.className=this.classNav;for(i=0;i<this.tabs.length;i++){t=this.tabs[i];t.headingText=t.div.title;if(this.removeTitle){t.div.title=\'\';}\r\n-if(!t.headingText){for(i2=0;i2<this.titleElements.length;i2++){headingElement=t.div.getElementsByTagName(this.titleElements[i2])[0];if(headingElement){t.headingText=headingElement.innerHTML;if(this.titleElementsStripHTML){t.headingText.replace(/ /gi," ");t.headingText=t.headingText.replace(/<[^>]+>/g,"");}\r\n-break;}}}\r\n-if(!t.headingText){t.headingText=i+1;}\r\n-DOM_li=document.createElement("li");t.li=DOM_li;DOM_a=document.createElement("a");DOM_a.appendChild(document.createTextNode(t.headingText));DOM_a.href="javascript:void(null);";DOM_a.title=t.headingText;DOM_a.onclick=this.navClick;DOM_a.tabber=this;DOM_a.tabberIndex=i;if(this.addLinkId&&this.linkIdFormat){aId=this.linkIdFormat;aId=aId.replace(/<tabberid>/gi,this.id);aId=aId.replace(/<tabnumberzero>/gi,i);aId=aId.replace(/<tabnumberone>/gi,i+1);aId=aId.replace(/<tabtitle>/gi,t.headingText.replace(/[^a-zA-Z0-9\\-]/gi,\'\'));DOM_a.id=aId;}\r\n-DOM_li.appendChild(DOM_a);DOM_ul.appendChild(DOM_li);}\r\n-e.insertBefore(DOM_ul,e.firstChild);e.className=e.className.replace(this.REclassMain,this.classMainLive);this.tabShow(defaultTab);if(typeof this.onLoad==\'function\'){this.onLoad({tabber:this});}\r\n-return this;};tabberObj.prototype.navClick=function(event)\r\n-{var\r\n-rVal,a,self,tabberIndex,onClickArgs;a=this;if(!a.tabber){return false;}\r\n-self=a.tabber;tabberIndex=a.tabberIndex;a.blur();if(typeof self.onClick==\'function\'){onClickArgs={\'tabber\':self,\'index\':tabberIndex,\'event\':event};if(!event){onClickArgs.event=window.event;}\r\n-rVal=self.onClick(onClickArgs);if(rVal===false){return false;}}\r\n-self.tabShow(tabberIndex);return false;};tabberObj.prototype.tabHideAll=function()\r\n-{var i;for(i=0;i<this.tabs.length;i++){this.tabHide(i);}};tabberObj.prototype.tabHide=function(tabberIndex)\r\n-{var div;if(!this.tabs[tabberIndex]){return false;}\r\n-div=this.tabs[tabberIndex].div;if(!div.className.match(this.REclassTabHide)){div.className+=\' \'+this.classTabHide;}\r\n-this.navClearActive(tabberIndex);return this;};tabberObj.prototype.tabShow=function(tabberIndex)\r\n-{var div;if(!this.tabs[tabberIndex]){return false;}\r\n-this.tabHideAll();div=this.tabs[tabberIndex].div;div.className=div.className.replace(this.REclassTabHide,\'\');this.navSetActive(tabberIndex);if(typeof this.onTabDisplay==\'function\'){this.onTabDisplay({\'tabber\':this,\'index\':tabberIndex});}\r\n-return this;};tabberObj.prototype.n'..b'var\n+childNodes,i,i2,t,defaultTab=0,DOM_ul,DOM_li,DOM_a,aId,headingElement;if(!document.getElementsByTagName){return false;}\n+if(e.id){this.id=e.id;}\n+this.tabs.length=0;childNodes=e.childNodes;for(i=0;i<childNodes.length;i++){if(childNodes[i].className&&childNodes[i].className.match(this.REclassTab)){t=new Object();t.div=childNodes[i];this.tabs[this.tabs.length]=t;if(childNodes[i].className.match(this.REclassTabDefault)){defaultTab=this.tabs.length-1;}}}\n+DOM_ul=document.createElement("ul");DOM_ul.className=this.classNav;for(i=0;i<this.tabs.length;i++){t=this.tabs[i];t.headingText=t.div.title;if(this.removeTitle){t.div.title=\'\';}\n+if(!t.headingText){for(i2=0;i2<this.titleElements.length;i2++){headingElement=t.div.getElementsByTagName(this.titleElements[i2])[0];if(headingElement){t.headingText=headingElement.innerHTML;if(this.titleElementsStripHTML){t.headingText.replace(/ /gi," ");t.headingText=t.headingText.replace(/<[^>]+>/g,"");}\n+break;}}}\n+if(!t.headingText){t.headingText=i+1;}\n+DOM_li=document.createElement("li");t.li=DOM_li;DOM_a=document.createElement("a");DOM_a.appendChild(document.createTextNode(t.headingText));DOM_a.href="javascript:void(null);";DOM_a.title=t.headingText;DOM_a.onclick=this.navClick;DOM_a.tabber=this;DOM_a.tabberIndex=i;if(this.addLinkId&&this.linkIdFormat){aId=this.linkIdFormat;aId=aId.replace(/<tabberid>/gi,this.id);aId=aId.replace(/<tabnumberzero>/gi,i);aId=aId.replace(/<tabnumberone>/gi,i+1);aId=aId.replace(/<tabtitle>/gi,t.headingText.replace(/[^a-zA-Z0-9\\-]/gi,\'\'));DOM_a.id=aId;}\n+DOM_li.appendChild(DOM_a);DOM_ul.appendChild(DOM_li);}\n+e.insertBefore(DOM_ul,e.firstChild);e.className=e.className.replace(this.REclassMain,this.classMainLive);this.tabShow(defaultTab);if(typeof this.onLoad==\'function\'){this.onLoad({tabber:this});}\n+return this;};tabberObj.prototype.navClick=function(event)\n+{var\n+rVal,a,self,tabberIndex,onClickArgs;a=this;if(!a.tabber){return false;}\n+self=a.tabber;tabberIndex=a.tabberIndex;a.blur();if(typeof self.onClick==\'function\'){onClickArgs={\'tabber\':self,\'index\':tabberIndex,\'event\':event};if(!event){onClickArgs.event=window.event;}\n+rVal=self.onClick(onClickArgs);if(rVal===false){return false;}}\n+self.tabShow(tabberIndex);return false;};tabberObj.prototype.tabHideAll=function()\n+{var i;for(i=0;i<this.tabs.length;i++){this.tabHide(i);}};tabberObj.prototype.tabHide=function(tabberIndex)\n+{var div;if(!this.tabs[tabberIndex]){return false;}\n+div=this.tabs[tabberIndex].div;if(!div.className.match(this.REclassTabHide)){div.className+=\' \'+this.classTabHide;}\n+this.navClearActive(tabberIndex);return this;};tabberObj.prototype.tabShow=function(tabberIndex)\n+{var div;if(!this.tabs[tabberIndex]){return false;}\n+this.tabHideAll();div=this.tabs[tabberIndex].div;div.className=div.className.replace(this.REclassTabHide,\'\');this.navSetActive(tabberIndex);if(typeof this.onTabDisplay==\'function\'){this.onTabDisplay({\'tabber\':this,\'index\':tabberIndex});}\n+return this;};tabberObj.prototype.navSetActive=function(tabberIndex)\n+{this.tabs[tabberIndex].li.className=this.classNavActive;return this;};tabberObj.prototype.navClearActive=function(tabberIndex)\n+{this.tabs[tabberIndex].li.className=\'\';return this;};function tabberAutomatic(tabberArgs)\n+{var\n+tempObj,divs,i;if(!tabberArgs){tabberArgs={};}\n+tempObj=new tabberObj(tabberArgs);divs=document.getElementsByTagName("div");for(i=0;i<divs.length;i++){if(divs[i].className&&divs[i].className.match(tempObj.REclassMain)){tabberArgs.div=divs[i];divs[i].tabber=new tabberObj(tabberArgs);}}\n+return this;}\n+function tabberAutomaticOnLoad(tabberArgs)\n+{var oldOnLoad;if(!tabberArgs){tabberArgs={};}\n+oldOnLoad=window.onload;if(typeof window.onload!=\'function\'){window.onload=function(){tabberAutomatic(tabberArgs);};}else{window.onload=function(){oldOnLoad();tabberAutomatic(tabberArgs);};}}\n if(typeof tabberOptions==\'undefined\'){tabberAutomaticOnLoad();}else{if(!tabberOptions[\'manualStartup\']){tabberAutomaticOnLoad(tabberOptions);}}\n\\ No newline at end of file\n'

diff -r 942eea8359fe -r 4d2a8f98a502 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Dec 08 06:32:16 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,36 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
- <package name="igblastwrp" version="0.6">
- <install version="1.0">
- <actions>
- <action type="download_by_url">https://github.com/mikessh/higblast/releases/download/v0.6/igblastwrapper_linux64.tar.gz</action>
- <action type="move_file">
- <source>bin</source>
- <destination>$INSTALL_DIR/</destination>
- </action>
- <action type="move_file">
- <source>data</source>
- <destination>$INSTALL_DIR/</destination>
- </action>
- <action type="move_file">
- <source>igblastwrp.jar</source>
- <destination>$INSTALL_DIR/</destination>
- </action>
- <action type="set_environment">
- <environment_variable action="set_to" name="IGBLASTWRP">$INSTALL_DIR/</environment_variable>
- </action>
- </actions>
- </install>
- <readme>
-Downloads https://github.com/mikessh/higblast/
- </readme>
- </package>
- <package name="weblogo" version="3.3">
- <repository changeset_revision="648e4b32f15c" name="package_weblogo_3_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
- </package>
- 
-</tool_dependency>