Mercurial > repos > nml > pangolin
changeset 1:b91b3923656e draft
"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 216d09e3d63a6ab4245df78c111ca97d4e0b14de"
| author | nml |
|---|---|
| date | Fri, 01 May 2020 15:33:17 -0400 |
| parents | f612c8391bd8 |
| children | c897e502c084 |
| files | pangolin.xml test-data/lineage_report.csv test-data/lineage_report.tsv |
| diffstat | 3 files changed, 12 insertions(+), 11 deletions(-) [+] |
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--- a/pangolin.xml Fri May 01 11:30:48 2020 -0400 +++ b/pangolin.xml Fri May 01 15:33:17 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="pangolon" name="Pangolin" version="@VERSION@+galaxy0"> +<tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0"> <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</description> <macros> <import>macros.xml</import> @@ -6,8 +6,9 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ -pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' +pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' && +sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv ]]></command> <inputs> <param name="input1" type="data" format="fasta" @@ -25,12 +26,12 @@ </section> </inputs> <outputs> - <data format="csv" from_work_dir="lineage_report.csv" name="lineage_report" label="${input1.name}_lineage_report" /> + <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" /> </outputs> <tests> <test> <param name="input1" value="test_seqs.fasta" /> - <output name="lineage_report" value="lineage_report.csv" /> + <output name="lineage_report" value="lineage_report.tsv" /> </test> </tests> <help><![CDATA[
--- a/test-data/lineage_report.csv Fri May 01 11:30:48 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -taxon,lineage,SH-alrt,UFbootstrap,lineages_version,status,note -Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17,B,100,100,2020-04-27,passed_qc, -USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16,B.1,100,100,2020-04-27,passed_qc, -This_seq_has_no_seq,None,0,0,2020-04-27,fail,seq_len:0 -This_seq_is_too_short,None,0,0,2020-04-27,fail,seq_len:2997 -This_seq_has_lots_of_Ns,None,0,0,2020-04-27,fail,N_content:0.98 -This_seq_is_literally_just_N,None,0,0,2020-04-27,fail,N_content:1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage_report.tsv Fri May 01 15:33:17 2020 -0400 @@ -0,0 +1,7 @@ +taxon lineage SH-alrt UFbootstrap lineages_version status note +Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17 B 100 100 2020-04-27 passed_qc +USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16 B.1 100 100 2020-04-27 passed_qc +This_seq_has_no_seq None 0 0 2020-04-27 fail seq_len:0 +This_seq_is_too_short None 0 0 2020-04-27 fail seq_len:2997 +This_seq_has_lots_of_Ns None 0 0 2020-04-27 fail N_content:0.98 +This_seq_is_literally_just_N None 0 0 2020-04-27 fail N_content:1.0