Mercurial > repos > azomics > autospill
changeset 2:3293c160f73c draft default tip
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/autospill commit 71a5a8cb5b80c7971440a2a1c49a68d311366c6f"
| author | azomics |
|---|---|
| date | Tue, 29 Jun 2021 23:53:54 +0000 |
| parents | 7f5bf24d5aeb |
| children | |
| files | autospill.xml |
| diffstat | 1 files changed, 10 insertions(+), 2 deletions(-) [+] |
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--- a/autospill.xml Sat Jun 19 10:57:45 2021 +0000 +++ b/autospill.xml Tue Jun 29 23:53:54 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="autospill" name="Autospill" version="0.2.0+galaxy0" profile="19.01" python_template_version="3.5"> +<tool id="autospill" name="Autospill" version="0.2.0+galaxy1" profile="19.01" python_template_version="3.5"> <description> calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively </description> @@ -115,6 +115,13 @@ asp\$figure.convergence.dir <- "figure_convergence" asp\$table.spillover.dir <- "table_spillover" +#if $remove_forbidden: +for(c in strsplit('$remove_forbidden', split="")) { + print(paste0("Removing ",c," from forbidden characters...")) + asp\$marker.forbidden.char<-gsub(c, "", asp\$marker.forbidden.char) +} +#end if + ## Set workers through GALAXY_SLOTS asp\$worker.process.n<-args[[3]] @@ -166,6 +173,7 @@ <option value="paper">Paper</option> <option value="website">Website</option> </param> --> + <param type="text" name="remove_forbidden" value="" label="Remove characters from autospill's forbidden list of characters" help="Autospill considers all these characters ' !\#$%()*,/:;&?@[\]^{|}~ plus double quotes as forbidden characters. List any of them here to remove them from that list - at a risk of breaking execution." /> <param type="boolean" name="get_figure_scatter" label="Get scatter" help="If turned On, the tool will produce scatter plots between setups" checked="true"/> <param type="boolean" name="get_error" label="Get error matrices/tables" help="If turned On, the tool will produce error matrices for intercepts, coefficients, slope and skewness" checked="false"/> <param type="boolean" name="get_gates" label="Get gating information" help="If turned On, gating parameters information will be produced" checked="true"/> @@ -229,7 +237,7 @@ - Collection of control FCS files - Auxiliary control file: Contains metadata for control list. It has to match original names of FCS files uploaded, and those files need to be present in the Collection of control FCS files given. - +- Optional list of characters to remove from autospill's forbidden characters (that otherwise autospill replaces with '-'). **Output**