Mercurial > repos > nml > pangolin
changeset 5:e2497d4385e2 draft default tip
"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 9e569ed56e07b5d2d3fb8a72ddc477d34570f081"
| author | nml |
|---|---|
| date | Fri, 29 May 2020 00:37:50 -0400 |
| parents | 35566aadcfc7 |
| children | |
| files | macros.xml pangolin.xml |
| diffstat | 2 files changed, 10 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Thu May 14 20:53:17 2020 -0400 +++ b/macros.xml Fri May 29 00:37:50 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">1.1.13</token> + <token name="@VERSION@">1.1.14</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">pangolin</requirement>
--- a/pangolin.xml Thu May 14 20:53:17 2020 -0400 +++ b/pangolin.xml Fri May 29 00:37:50 2020 -0400 @@ -6,7 +6,7 @@ <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' $additional.write_tree && +pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' $additional.write_tree $additional.include_putative && sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv ]]></command> @@ -23,6 +23,13 @@ label="Minimum query length to attempt assignment" argument="--min-length" /> + <param name="include_putative" type="boolean" checked="false" argument="-p" + truevalue="-p" + falsevalue="" + label="Include putative lineages" + help="Putative lineages fit the criteria required for lineage designation but have not got recall values suitable for lineage assignment. + If left as 'No', only lineages with >95% recall rate will be used." + /> <param name="write_tree" type="boolean" checked="false" truevalue="--write-tree" falsevalue="" @@ -54,6 +61,7 @@ <param name="input1" value="test_seqs.fasta" /> <section name="additional"> <param name="write_tree" value="true" /> + <param name="include_putative" value="true" /> </section> <output name="lineage_report" > <assert_contents>