| Previous changeset 5:012a738edf5a (2016-11-01) Next changeset 7:ad9be244b104 (2016-11-07) |
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modified:
shm_csr.xml wrapper.sh |
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| diff -r 012a738edf5a -r 2ddb9a21f635 shm_csr.xml --- a/shm_csr.xml Tue Nov 01 10:15:37 2016 -0400 +++ b/shm_csr.xml Tue Nov 01 10:48:38 2016 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0"> <description></description> <command interpreter="bash"> - wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter $empty_region_filter $fast + wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter $empty_region_filter $fast </command> <inputs> <param name="in_file" type="data" label="IMGT zip file to be analysed" /> @@ -66,6 +66,9 @@ <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> </data> + <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" > + <filter>naive_output_cond['naive_output'] == "yes"</filter> + </data> </outputs> <citations> <citation type="doi">10.1093/nar/gks457</citation> |
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| diff -r 012a738edf5a -r 2ddb9a21f635 wrapper.sh --- a/wrapper.sh Tue Nov 01 10:15:37 2016 -0400 +++ b/wrapper.sh Tue Nov 01 10:48:38 2016 -0400 |
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| @@ -13,10 +13,11 @@ naive_output_ca=$9 naive_output_cg=${10} naive_output_cm=${11} -filter_unique=${12} -class_filter=${13} -empty_region_filter=${14} -fast=${15} +naive_output_ce=${12} +filter_unique=${13} +class_filter=${14} +empty_region_filter=${15} +fast=${16} mkdir $outdir tar -xzf $dir/style.tar.gz -C $outdir @@ -371,12 +372,14 @@ echo "<img src='aa_histogram_IGA.png'/><br />" >> $output echo "<img src='aa_histogram_IGG.png'/><br />" >> $output echo "<img src='aa_histogram_IGM.png'/><br />" >> $output + echo "<img src='aa_histogram_IGE.png'/><br />" >> $output fi echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output +echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output echo "</div>" >> $output #antigen selection tab end @@ -434,6 +437,14 @@ echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" fi + if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt + bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt + else + echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt" + echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" + fi + PWD="$tmp" echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab @@ -464,15 +475,19 @@ clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output echo "</div>" >> $output -echo "<div class='tabbertab' title='Ca'>" >> $output +echo "<div class='tabbertab' title='IGA'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output echo "</div>" >> $output -echo "<div class='tabbertab' title='Cg'>" >> $output +echo "<div class='tabbertab' title='IGG'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output echo "</div>" >> $output -echo "<div class='tabbertab' title='Cm'>" >> $output +echo "<div class='tabbertab' title='IGM'>" >> $output +clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output +echo "</div>" >> $output + +echo "<div class='tabbertab' title='IGE'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output echo "</div>" >> $output @@ -520,6 +535,7 @@ echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transition_IGE_sum.txt' download='transition_IGE_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output @@ -533,6 +549,7 @@ echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output @@ -548,6 +565,8 @@ echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output @@ -560,6 +579,7 @@ echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output echo "</table>" >> $output @@ -611,6 +631,14 @@ echo "No IGM sequences" > "$outdir/baseline_IGM.txt" fi + mkdir $outdir/baseline/IGE + if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then + cd $outdir/baseline/IGE + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt" + else + echo "No IGE sequences" > "$outdir/baseline_IGE.txt" + fi + cd $tmp echo "Cleaning up *.RData files" @@ -626,6 +654,7 @@ cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} + cp $outdir/new_IMGT_IGE.txz ${naive_output_ce} fi echo "</table>" >> $outdir/base_overview.html |