Mercurial > repos > davidvanzessen > shm_csr
changeset 84:4db34e32dd47 draft
"planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
| author | rhpvorderman |
|---|---|
| date | Wed, 27 Oct 2021 09:38:20 +0000 |
| parents | 729738462297 |
| children | a539d14d66b6 |
| files | CHANGELOG.md conda_environment.yml container/involucro remove_files.txt shm_csr.xml tests/.pytest_cache/.gitignore tests/.pytest_cache/CACHEDIR.TAG tests/.pytest_cache/README.md tests/.pytest_cache/v/cache/nodeids tests/.pytest_cache/v/cache/stepwise tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.4.pyc tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc wrapper.sh |
| diffstat | 13 files changed, 191 insertions(+), 36 deletions(-) [+] |
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--- a/CHANGELOG.md Wed Sep 15 12:24:06 2021 +0000 +++ b/CHANGELOG.md Wed Oct 27 09:38:20 2021 +0000 @@ -1,3 +1,8 @@ +version 1.2.0 +------------- ++ Add a container in which the tool can execute. ++ Remove redundant files after execution. + version 1.1.0 ------------- + Added changeo as a dependency. Porting to python3 was necessary to achieve
--- a/conda_environment.yml Wed Sep 15 12:24:06 2021 +0000 +++ b/conda_environment.yml Wed Oct 27 09:38:20 2021 +0000 @@ -4,7 +4,7 @@ - bioconda - defaults dependencies: - - python=3.7 + - python=3.7.1 - changeo=0.4.4 - biopython=1.72 # Higher versions break changeo - unzip=6.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove_files.txt Wed Oct 27 09:38:20 2021 +0000 @@ -0,0 +1,171 @@ +results/aa_histogram.txt +results/aa_histogram_absent.txt +results/aa_histogram_absent_IGA.txt +results/aa_histogram_absent_IGG.txt +results/aa_histogram_absent_IGM.txt +results/aa_histogram_count.txt +results/aa_histogram_count_IGA.txt +results/aa_histogram_count_IGG.txt +results/aa_histogram_count_IGM.txt +results/aa_histogram_IGA.txt +results/aa_histogram_IGG.txt +results/aa_histogram_IGM.txt +results/after_unique_filter.txt +results/all_mean_n.txt +results/all_mean_value.txt +results/all_median_n.txt +results/all_median_value.txt +results/all_sum_n.txt +results/all_sum_value.txt +results/before_filters.txt +results/before_unique_filter.txt +results/data_sum.txt +results/filtering_steps.txt +results/hotspot_analysis_mean.txt +results/hotspot_analysis_median.txt +results/hotspot_analysis_sum.txt +results/identified_genes.txt +results/IGA1_mean_n.txt +results/IGA1_mean_value.txt +results/IGA1_median_n.txt +results/IGA1_median_value.txt +results/IGA1_sum_n.txt +results/IGA1_sum_value.txt +results/IGA2_mean_n.txt +results/IGA2_mean_value.txt +results/IGA2_median_n.txt +results/IGA2_median_value.txt +results/IGA2_sum_n.txt +results/IGA2_sum_value.txt +results/IGA_mean_n.txt +results/IGA_mean_value.txt +results/IGA_median_n.txt +results/IGA_median_value.txt +results/IGA_sum_n.txt +results/IGA_sum_value.txt +results/IGE_mean_n.txt +results/IGE_mean_value.txt +results/IGE_median_n.txt +results/IGE_median_value.txt +results/IGE_sum_n.txt +results/IGE_sum_value.txt +results/IGG1_mean_n.txt +results/IGG1_mean_value.txt +results/IGG1_median_n.txt +results/IGG1_median_value.txt +results/IGG1_sum_n.txt +results/IGG1_sum_value.txt +results/IGG2_mean_n.txt +results/IGG2_mean_value.txt +results/IGG2_median_n.txt +results/IGG2_median_value.txt +results/IGG2_sum_n.txt +results/IGG2_sum_value.txt +results/IGG3_mean_n.txt +results/IGG3_mean_value.txt +results/IGG3_median_n.txt +results/IGG3_median_value.txt +results/IGG3_sum_n.txt +results/IGG3_sum_value.txt +results/IGG4_mean_n.txt +results/IGG4_mean_value.txt +results/IGG4_median_n.txt +results/IGG4_median_value.txt +results/IGG4_sum_n.txt +results/IGG4_sum_value.txt +results/IGG_mean_n.txt +results/IGG_mean_value.txt +results/IGG_median_n.txt +results/IGG_median_value.txt +results/IGG_sum_n.txt +results/IGG_sum_value.txt +results/IGM_mean_n.txt +results/IGM_mean_value.txt +results/IGM_median_n.txt +results/IGM_median_value.txt +results/IGM_sum_n.txt +results/IGM_sum_value.txt +results/matched_all_mean.txt +results/matched_all_median.txt +results/matched_IGA1_mean.txt +results/matched_IGA1_median.txt +results/matched_IGA2_mean.txt +results/matched_IGA2_median.txt +results/matched_IGA_mean.txt +results/matched_IGA_median.txt +results/matched_IGE_mean.txt +results/matched_IGE_median.txt +results/matched_IGG1_mean.txt +results/matched_IGG1_median.txt +results/matched_IGG2_mean.txt +results/matched_IGG2_median.txt +results/matched_IGG3_mean.txt +results/matched_IGG3_median.txt +results/matched_IGG4_mean.txt +results/matched_IGG4_median.txt +results/matched_IGG_mean.txt +results/matched_IGG_median.txt +results/matched_IGM_mean.txt +results/matched_IGM_median.txt +results/matched_unmatched_mean.txt +results/matched_unmatched_median.txt +results/matched_unmatched_sum.txt +results/mutationdict.txt +results/mutation_in_motifs.txt +results/mutations_mean.txt +results/mutations_median.txt +results/mutations_sum.txt +results/RGYW.txt +results/shm_overview_tandem_row.txt +results/tandem_frequency.txt +results/transitions_all_mean.txt +results/transitions_all_median.txt +results/transitions_IGA1_mean.txt +results/transitions_IGA1_median.txt +results/transitions_IGA2_mean.txt +results/transitions_IGA2_median.txt +results/transitions_IGA_mean.txt +results/transitions_IGA_median.txt +results/transitions_IGE_mean.txt +results/transitions_IGE_median.txt +results/transitions_IGG1_mean.txt +results/transitions_IGG1_median.txt +results/transitions_IGG2_mean.txt +results/transitions_IGG2_median.txt +results/transitions_IGG3_mean.txt +results/transitions_IGG3_median.txt +results/transitions_IGG4_mean.txt +results/transitions_IGG4_median.txt +results/transitions_IGG_mean.txt +results/transitions_IGG_median.txt +results/transitions_IGM_mean.txt +results/transitions_IGM_median.txt +results/transitions_unmatched_mean.txt +results/transitions_unmatched_median.txt +results/transitions_unmatched_sum.txt +results/unmatched_mean_n.txt +results/unmatched_mean_value.txt +results/unmatched_median_n.txt +results/unmatched_median_value.txt +results/unmatched_sum_n.txt +results/unmatched_sum_value.txt +results/change_o/change-o-db.txt +results/change_o/change-o-db-defined_first_clones.txt +results/change_o/change-o-db-defined_first_clones-IGA.txt +results/change_o/change-o-db-defined_first_clones-IGG.txt +results/change_o/change-o-db-defined_first_clones-IGM.txt +results/change_o/change-o-db-IGA.txt +results/change_o/change-o-db-IGG.txt +results/change_o/change-o-db-IGM.txt +results/change_o/input.tab +aa.txt +aa_change_stats.txt +gapped_aa.txt +gapped_nt.txt +hotspots.txt +junction.txt +mutationanalysis.txt +mutationstats.txt +sequences.txt +summary.txt +Rplots.pdf
--- a/shm_csr.xml Wed Sep 15 12:24:06 2021 +0000 +++ b/shm_csr.xml Wed Oct 27 09:38:20 2021 +0000 @@ -1,7 +1,7 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.1"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.2"> <description></description> <requirements> - <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="3.7.1">python</requirement> <requirement type="package" version="0.4.4">changeo</requirement> <!--Biopython should be set at a version at the release of changeo 0.4.4. Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.--> @@ -16,6 +16,7 @@ <requirement type="package" version="4.4.18">bash</requirement> <requirement type="package" version="1.34">tar</requirement> <requirement type="package" version="5.39">file</requirement> + <container type="docker">quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container> </requirements> <command interpreter="bash"> #if str ( $filter_unique.filter_unique_select ) == "remove":
--- a/tests/.pytest_cache/.gitignore Wed Sep 15 12:24:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -# Created by pytest automatically. -*
--- a/tests/.pytest_cache/CACHEDIR.TAG Wed Sep 15 12:24:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Signature: 8a477f597d28d172789f06886806bc55 -# This file is a cache directory tag created by pytest. -# For information about cache directory tags, see: -# http://www.bford.info/cachedir/spec.html
--- a/tests/.pytest_cache/README.md Wed Sep 15 12:24:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -# pytest cache directory # - -This directory contains data from the pytest's cache plugin, -which provides the `--lf` and `--ff` options, as well as the `cache` fixture. - -**Do not** commit this to version control. - -See [the docs](https://docs.pytest.org/en/stable/cache.html) for more information.
--- a/tests/.pytest_cache/v/cache/nodeids Wed Sep 15 12:24:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -[ - "test_shm_csr.py::test_aa_histogram_sum" -] \ No newline at end of file
--- a/tests/.pytest_cache/v/cache/stepwise Wed Sep 15 12:24:06 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -[] \ No newline at end of file
--- a/wrapper.sh Wed Sep 15 12:24:06 2021 +0000 +++ b/wrapper.sh Wed Oct 27 09:38:20 2021 +0000 @@ -892,6 +892,17 @@ IFS="$tIFS" +echo "---------------- remove_files----------------" +echo "---------------- remove_files----------------<br />" >> $log + +rm -r -v results/baseline +rm -r -v files +filename='remove_files.txt' + +while read file; do + rm -v $file +done < "$filename" + echo "---------------- Done! ----------------" echo "---------------- Done! ----------------<br />" >> $outdir/log.html @@ -901,18 +912,3 @@ - - - - - - - - - - - - - - -