Mercurial > repos > davidvanzessen > shm_csr
changeset 91:f387cc1580c6 draft
"planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690"
| author | rhpvorderman |
|---|---|
| date | Wed, 02 Feb 2022 10:57:36 +0000 |
| parents | 6809c63d9161 |
| children | cf8ad181628f |
| files | CHANGELOG.md shm_csr.xml tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc wrapper.sh |
| diffstat | 4 files changed, 29 insertions(+), 1 deletions(-) [+] |
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--- a/CHANGELOG.md Tue Jan 25 11:28:29 2022 +0000 +++ b/CHANGELOG.md Wed Feb 02 10:57:36 2022 +0000 @@ -1,3 +1,7 @@ +version 1.5.0 +------------- ++ Add an option to download all output files in a zip file. + version 1.4.0 ------------- + Fix a bug where synonymous mutations where incorrectly parsed.
--- a/shm_csr.xml Tue Jan 25 11:28:29 2022 +0000 +++ b/shm_csr.xml Wed Feb 02 10:57:36 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.4.0"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.5.0"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement>
--- a/wrapper.sh Tue Jan 25 11:28:29 2022 +0000 +++ b/wrapper.sh Wed Feb 02 10:57:36 2022 +0000 @@ -740,10 +740,34 @@ fi +# Use python's zipfile utility to prevent needing another dependency in the +# container. +current_dir=$(pwd) +cd $outdir +python -m zipfile -c all_outputs.zip \ + merged.txt filtered.txt unmatched.txt shm_overview.txt motif_per_seq.txt \ + mutation_by_id.txt base_overview.html aid_motives.txt relative_mutations.txt \ + absolute_mutations.txt tandems_by_id.txt scatter.txt frequency_ranges_class.txt \ + frequency_ranges_subclasses.txt transitions_all_sum.txt transitions_IGA_sum.txt \ + transitions_IGA1_sum.txt transitions_IGA2_sum.txt transitions_IGG_sum.txt \ + transitions_IGG1_sum.txt transitions_IGG2_sum.txt transitions_IGG3_sum.txt \ + transitions_IGG4_sum.txt transitions_IGM_sum.txt transitions_IGE_sum.txt \ + aa_id_mutations.txt absent_aa_id.txt aa_histogram_sum.txt \ + aa_histogram_sum_IGA.txt aa_histogram_sum_IGG.txt aa_histogram_sum_IGM.txt \ + aa_histogram_sum_IGE.txt baseline.txt baseline_IGA.pdf baseline_IGA.txt \ + baseline_IGG.pdf baseline_IGG.txt baseline_IGM.pdf baseline_IGM.txt \ + baseline_IGE.pdf baseline_IGE.txt IGA_pie.txt IGG_pie.txt \ + sequence_overview/index.html change_o/change-o-db-defined_clones*.txt \ + *.txz + +cd $current_dir + + echo "<div class='tabbertab' title='Downloads'>" >> $output echo "<table class='pure-table pure-table-striped'>" >> $output echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output +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 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output