Mercurial > repos > recetox > ramclustr_csv
changeset 1:d9c9ec0e2bd8 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
| author | recetox |
|---|---|
| date | Wed, 13 Jan 2021 11:42:34 +0000 |
| parents | 43b60b28ccf7 |
| children | 08b09930cd73 |
| files | ramclustr_csv.xml ramclustr_macros.xml ramclustr_wrapper.R |
| diffstat | 3 files changed, 17 insertions(+), 6 deletions(-) [+] |
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--- a/ramclustr_csv.xml Mon Dec 07 22:14:48 2020 +0000 +++ b/ramclustr_csv.xml Wed Jan 13 11:42:34 2021 +0000 @@ -10,7 +10,7 @@ <inputs> <expand macro="parameters_csv" /> <expand macro="parameters_required" /> - <expand macro="parameters_optional" /> + <expand macro="parameters_optional_csv" /> </inputs> <command detect_errors="aggressive"><![CDATA[ @@ -37,9 +37,7 @@ cor_method = "$required.cor_method", rt_only_low_n = $required.rt_only_low_n, replace_zeros = $required.replace_zeros, - #if $optional.st - st = $optional.st, - #end if + st = $ms_csv.st, #if $optional.maxt maxt = $optional.maxt, #end if
--- a/ramclustr_macros.xml Mon Dec 07 22:14:48 2020 +0000 +++ b/ramclustr_macros.xml Wed Jan 13 11:42:34 2021 +0000 @@ -8,6 +8,8 @@ <param label="sample_name_column" name="sample_name_column" type="integer" value="1" help="which column from the csv file contains sample names?" /> <param label="feature_delimiter" name="feature_delimiter" type="text" value="_" help="Only required if ms input is set! How feature mz and rt are delimited in csv import column header e.g. ='-'" /> <param label="retention_time_column" name="retention_time_column" type="integer" value="2" help="which position in delimited column header represents the retention time (csv only)" /> + <param label="st" name="st" type="float" value="1" help="sigma t - time similarity decay value. A recommended starting point is half the value of + your average chromatographic peak width at half max (seconds))." /> </section> </xml> @@ -64,9 +66,17 @@ </section> </xml> - <xml name="parameters_optional"> + <xml name="parameters_optional_xcms"> <section name="optional" title="Optional Parameters" expanded="false"> - <param label="st" name="st" type="float" optional="true" help="sigma t - time similarity decay value " /> + <param label="st" name="st" type="float" optional="true" help="sigma t - time similarity decay value. A recommended starting point is half the value of + your average chromatographic peak width at half max (seconds))." /> + <param label="fftempdir" name="fftempdir" type="text" optional="true" help="valid path: if there are file size limitations on the default ff pacakge temp directory - getOptions('fftempdir') - you can change the directory used as the fftempdir with this option." /> + <param label="maxt" name="maxt" type="integer" optional="true" help="maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero" /> + </section> + </xml> + + <xml name="parameters_optional_csv"> + <section name="optional" title="Optional Parameters" expanded="false"> <param label="fftempdir" name="fftempdir" type="text" optional="true" help="valid path: if there are file size limitations on the default ff pacakge temp directory - getOptions('fftempdir') - you can change the directory used as the fftempdir with this option." /> <param label="maxt" name="maxt" type="integer" optional="true" help="maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero" /> </section>