Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 70:6fdafffd7f0f draft
Uploaded
author | davidvanzessen |
---|---|
date | Wed, 17 Aug 2016 08:16:55 -0400 |
parents | a59de79f6c0f |
children | 55d06821d6a5 |
files | report_clonality/r_wrapper.sh report_clonality_igg.xml |
diffstat | 2 files changed, 13 insertions(+), 11 deletions(-) [+] |
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--- a/report_clonality/r_wrapper.sh Mon Aug 08 08:53:33 2016 -0400 +++ b/report_clonality/r_wrapper.sh Wed Aug 17 08:16:55 2016 -0400 @@ -89,6 +89,7 @@ fi done echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile +echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $outputFile echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile @@ -158,8 +159,8 @@ if [[ "${clonality_method}" == "old" ]] ; then echo "in old" clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" - echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile - echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile + echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile + echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile #replicate,reads,squared echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile @@ -207,28 +208,28 @@ #if [[ "$hasJunctionData" == "Yes" ]] ; then if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do echo "<tr><td>$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></tr>" >> $outputFile done < $outputDir/junctionAnalysisProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do echo "<tr><td>$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></tr>" >> $outputFile done < $outputDir/junctionAnalysisUnProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do echo "<tr><td>$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></tr>" >> $outputFile done < $outputDir/junctionAnalysisProd_median.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do echo "<tr><td>$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></tr>" >> $outputFile @@ -249,8 +250,8 @@ echo "</div></div>" >> $outputFile echo "<div class='tabbertab' title='Downloads'>" >> $outputFile -echo "<table border='1'>" >> $outputFile -echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile +echo "<table class='pure-table pure-table-striped'>" >> $outputFile +echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
--- a/report_clonality_igg.xml Mon Aug 08 08:53:33 2016 -0400 +++ b/report_clonality_igg.xml Wed Aug 17 08:16:55 2016 -0400 @@ -11,11 +11,12 @@ <param name="in_file" format="tabular" type="data" label="Data to Process" /> <param name="clonaltype" type="select" label="Clonal Type Definition (Needed for clonality calculation)"> <option value="none">Don't remove duplicates based on clonaltype</option> - <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.AA.Seq</option> <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> - <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.AA.Seq</option> <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option> + <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.AA.DNA</option> </param> <conditional name="gene_selection" > @@ -85,7 +86,7 @@ </when> </conditional> - <param name="filterproductive" type="select" label="Filter out the unproductive sequences"> + <param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs "> <option value="yes">Yes</option> <option value="no">No</option> </param>