Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 19:3ef457aa5df6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 22 Dec 2016 03:43:02 -0500
parents 5d11c9139a55
children 9185c3dfc679
files complete_immunerepertoire.xml report_clonality/naive_compare.htm report_clonality/naive_downloads.htm report_clonality/r_wrapper.sh
diffstat 4 files changed, 15 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/complete_immunerepertoire.xml	Wed Dec 21 11:53:03 2016 -0500
+++ b/complete_immunerepertoire.xml	Thu Dec 22 03:43:02 2016 -0500
@@ -128,13 +128,13 @@
 **Input files**
 
 IMGT/HighV-QUEST .zip and .txz files and FASTA files are accepted as input files. In addition filtered IMGT files generated using the SHM & CSR pipeline can be used as input files. 
-Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files  “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
+Note: Files can be uploaded by using “get data” and “upload file”. When uploading IMGT files  “IMGT archive“ should be selected as a file type. When uploading FASTA files the auto-detect function can be used to select a file type. Special characters should be prevented in the file names of the uploaded replicates as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
 
 -----
 
 **Donor and replicates**
 
-The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one sample can be uploaded. However, multiple samples per donor can be uploaded by using the insert sample button. In addition, multiple donors van be added by using the insert donor button. The multiple sample option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 samples have to be included per donor. 
+The immune repertoire pipeline can analyse files from multiple donors in parallel. Therefore for each analysed donor an ID has to be given. This ID can only contain letters, numbers and _. Spaces in the ID give an error when running the immune repertoire pipeline. In the default setting of the immune repertoire pipeline one donor consisting out of one replicate can be uploaded. However, multiple replicates per donor can be uploaded by using the "Add new replicate" button. In addition, multiple donors van be added by using the insert donor button. The multiple replicate option can be used when multiple data files from the same donor are available. For the calculation of the clonality score using the algorithm described by Boyd et al (PMID: 20161664) at least 3 replicates have to be included per donor. 
 
 -----
 
@@ -156,7 +156,7 @@
 
 **Species**
 
-Enter the species of the sample you would like to analyse.
+Enter the species of the replicates(s) you would like to analyse.
 
 -----
 
@@ -174,7 +174,7 @@
 
 **Shared clonal types / clonality**
 
-This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a sample no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
+This filter allows you do identify overlapping sequences between different replicates. If you only upload a single replicate from a replicate no sequences overlap or clonality can be determined and therefore the “do not determine overlap” option should be selection. The “Determine the number of sequences that share the same clonal type between the replicates” option allows the user to determine the number of overlapping sequences (based on the clonal type definition defined in the ‘clonal type definition filter’) between different replicates. This can be used to for instance look at different time point in the same donor to changes in the repertoire. When three or more replicates of the same blood same are amplified and sequences in parallel, the “determine clonality of the donor” function can be used to calculate the number of overlapping sequences as well as the clonality score as described by Boyd et al, PMID: 20161664.
 
 -----
 
--- a/report_clonality/naive_compare.htm	Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/naive_compare.htm	Thu Dec 22 03:43:02 2016 -0500
@@ -49,7 +49,7 @@
 <p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
 "Times New Roman","serif"'>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 samples the heatmaps of these samples are visualized
+include box of multiple replicates the heatmaps of these replicates are visualized
 next to each other allowing easy comparison of heatmaps. </span></p>
 
 <p class=MsoNormal>&nbsp;</p>
--- a/report_clonality/naive_downloads.htm	Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/naive_downloads.htm	Thu Dec 22 03:43:02 2016 -0500
@@ -129,7 +129,7 @@
 
 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the DJ heatmap for sample name:</span></u><span
+data used to generate the DJ heatmap for donor name:</span></u><span
 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
 Downloads the data set used for the generation of the DJ heatmap. For each
 uploaded donor a separate download is generated.</span></p>
--- a/report_clonality/r_wrapper.sh	Wed Dec 21 11:53:03 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Thu Dec 22 03:43:02 2016 -0500
@@ -37,7 +37,7 @@
 
 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2
 echo "<table border = 1>" >> $2
-echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
+echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
 	do
 		echo "<tr><td>$sample</td>" >> $2
@@ -48,7 +48,7 @@
 		echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
 done < $outputDir/productive_counting.txt
 echo "</table><br />" >> $2
-echo "Table showing the number and percentage of (unique) productive and unproductive sequences per sample and per replicate. <br />" >> $2
+echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2
 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
 echo "</center></html>" >> $2
 
@@ -138,7 +138,7 @@
 echo "<img src='DReadingFrame.png'/>" >> $outputFile
 
 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
-echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
+echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
 while IFS=, read Sample median
 do
 	echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
@@ -242,6 +242,8 @@
 					echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
 			done < $outputDir/ReplicateSumReads_$sample.csv
 			
+			echo "<tr><td></td><td></td></tr>" >> $outputFile
+			
 			#overview
 			echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile
 			while IFS=, read type count weight weightedCount
@@ -280,28 +282,28 @@
 	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
 	echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisUnProd_mean.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysisProd_median.csv
 	echo "</tbody></table>" >> $outputFile
 	
-	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
+	echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile