Mercurial > repos > recetox > ramclustr_xcms

comparison ramclustr_macros.xml @ 1:8f4d04ad4acd draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
author recetox
date Wed, 13 Jan 2021 11:42:07 +0000
parents a0c69d354b96
children 405c8f8dc073
comparison
equal deleted inserted replaced
0:a0c69d354b96 1:8f4d04ad4acd
6 <param label="ms" name="ms" type="data" format="csv" help="Features as columns, rows as samples. Column header mz_rt" /> 6 <param label="ms" name="ms" type="data" format="csv" help="Features as columns, rows as samples. Column header mz_rt" />
7 <param label="idmsms" name="idmsms" type="data" format="csv" optional="true" help="Optional idMSMS / MSe csv data. same dim and names as ms required" /> 7 <param label="idmsms" name="idmsms" type="data" format="csv" optional="true" help="Optional idMSMS / MSe csv data. same dim and names as ms required" />
8 <param label="sample_name_column" name="sample_name_column" type="integer" value="1" help="which column from the csv file contains sample names?" /> 8 <param label="sample_name_column" name="sample_name_column" type="integer" value="1" help="which column from the csv file contains sample names?" />
9 <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. ='-'" /> 9 <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. ='-'" />
10 <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)" /> 10 <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)" />
11 <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
12 your average chromatographic peak width at half max (seconds))." />
11 </section> 13 </section>
12 </xml> 14 </xml>
13 15
14 <xml name="parameters_excluded"> 16 <xml name="parameters_excluded">
15 <param label="MStag" name="MStag" type="text" optional="true" help="character string in 'taglocation' to designat MS / MSe files e.g. '01.cdf'" /> 17 <param label="MStag" name="MStag" type="text" optional="true" help="character string in 'taglocation' to designat MS / MSe files e.g. '01.cdf'" />
62 <param label="replace_zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level set based on the detected signal intensities for that feature. " /> 64 <param label="replace_zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level set based on the detected signal intensities for that feature. " />
63 <param label="Merge MSP Files" name="merge_msp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="Whether to merge all msp in one file or export one msp per spectra"/> 65 <param label="Merge MSP Files" name="merge_msp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="Whether to merge all msp in one file or export one msp per spectra"/>
64 </section> 66 </section>
65 </xml> 67 </xml>
66 68
67 <xml name="parameters_optional"> 69 <xml name="parameters_optional_xcms">
68 <section name="optional" title="Optional Parameters" expanded="false"> 70 <section name="optional" title="Optional Parameters" expanded="false">
69 <param label="st" name="st" type="float" optional="true" help="sigma t - time similarity decay value " /> 71 <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
72 your average chromatographic peak width at half max (seconds))." />
73 <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." />
74 <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" />
75 </section>
76 </xml>
77
78 <xml name="parameters_optional_csv">
79 <section name="optional" title="Optional Parameters" expanded="false">
70 <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." /> 80 <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." />
71 <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" /> 81 <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" />
72 </section> 82 </section>
73 </xml> 83 </xml>
74 84