Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 91:f387cc1580c6 draft

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"planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690"
author rhpvorderman
date Wed, 02 Feb 2022 10:57:36 +0000
parents 6809c63d9161
children cf8ad181628f
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90:6809c63d9161 91:f387cc1580c6
738 738
739 echo "</div>" >> $output #clonality tab end 739 echo "</div>" >> $output #clonality tab end
740 740
741 fi 741 fi
742 742
743 # Use python's zipfile utility to prevent needing another dependency in the
744 # container.
745 current_dir=$(pwd)
746 cd $outdir
747 python -m zipfile -c all_outputs.zip \
748 merged.txt filtered.txt unmatched.txt shm_overview.txt motif_per_seq.txt \
749 mutation_by_id.txt base_overview.html aid_motives.txt relative_mutations.txt \
750 absolute_mutations.txt tandems_by_id.txt scatter.txt frequency_ranges_class.txt \
751 frequency_ranges_subclasses.txt transitions_all_sum.txt transitions_IGA_sum.txt \
752 transitions_IGA1_sum.txt transitions_IGA2_sum.txt transitions_IGG_sum.txt \
753 transitions_IGG1_sum.txt transitions_IGG2_sum.txt transitions_IGG3_sum.txt \
754 transitions_IGG4_sum.txt transitions_IGM_sum.txt transitions_IGE_sum.txt \
755 aa_id_mutations.txt absent_aa_id.txt aa_histogram_sum.txt \
756 aa_histogram_sum_IGA.txt aa_histogram_sum_IGG.txt aa_histogram_sum_IGM.txt \
757 aa_histogram_sum_IGE.txt baseline.txt baseline_IGA.pdf baseline_IGA.txt \
758 baseline_IGG.pdf baseline_IGG.txt baseline_IGM.pdf baseline_IGM.txt \
759 baseline_IGE.pdf baseline_IGE.txt IGA_pie.txt IGG_pie.txt \
760 sequence_overview/index.html change_o/change-o-db-defined_clones*.txt \
761 *.txz
762
763 cd $current_dir
764
765
743 echo "<div class='tabbertab' title='Downloads'>" >> $output 766 echo "<div class='tabbertab' title='Downloads'>" >> $output
744 767
745 echo "<table class='pure-table pure-table-striped'>" >> $output 768 echo "<table class='pure-table pure-table-striped'>" >> $output
746 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output 769 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
770 echo "<tr><td>All output files in a zip file</td><td><a href='all_outputs.zip' download='all_outputs.zip' >Download</a></td></tr>" >> $output
747 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output 771 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
748 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output 772 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
749 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output 773 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
750 774
751 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output 775 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output