Mercurial > repos > rhpvorderman > shm_csr
changeset 2:72d68e2e1fd3 draft
"planemo upload commit a8565b413cbe0ef70bc22994ecdd48b400ba6185"
| author | rhpvorderman |
|---|---|
| date | Fri, 05 Nov 2021 14:43:13 +0000 |
| parents | 281329c035ee |
| children | dced6d52d218 |
| files | conda_environment.yml shm_csr.xml tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc wrapper.sh |
| diffstat | 4 files changed, 12 insertions(+), 8 deletions(-) [+] |
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--- a/conda_environment.yml Fri Nov 05 10:59:28 2021 +0000 +++ b/conda_environment.yml Fri Nov 05 14:43:13 2021 +0000 @@ -17,7 +17,9 @@ - r-seqinr=3.4_5 - r-data.table=1.11.4 - file=5.39 + - bc=1.07.1 + - findutils=4.6.0 # Test dependencies below - - pytest + - pytest=6.2.5 # Add planemo so tool can be uploaded - - planemo + - planemo=0.74.9
--- a/shm_csr.xml Fri Nov 05 10:59:28 2021 +0000 +++ b/shm_csr.xml Fri Nov 05 14:43:13 2021 +0000 @@ -1,5 +1,5 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.2.2"> - <description>Performs a summary/analysis of an IMGT HighV-QUEST (https://www.imgt.org/HighV-QUEST/) ZIP file for Somatic hypermutation and class switch recombination.</description> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.1"> + <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> <requirement type="package" version="0.4.4">changeo</requirement> @@ -16,7 +16,9 @@ <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> - </requirements> + <requirement type="package" version="4.6.0">findutils</requirement> + <requirement type="package" version="1.07.1">bc</requirement> + </requirements> <command interpreter="bash"> #if str ( $filter_unique.filter_unique_select ) == "remove": wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
--- a/wrapper.sh Fri Nov 05 10:59:28 2021 +0000 +++ b/wrapper.sh Fri Nov 05 14:43:13 2021 +0000 @@ -895,12 +895,12 @@ echo "---------------- remove_files----------------" echo "---------------- remove_files----------------<br />" >> $log -rm -r -v results/baseline -rm -r -v files +rm -r -v -f results/baseline +rm -r -v -f files filename='remove_files.txt' while read file; do - rm -v $file + rm -v -f $file done < "$filename"