Mercurial > repos > iuc > micro_decon
comparison macros.xml @ 0:bd267e082f86 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon/ commit bb37578aa61bf4a47af262e02baf0a1c1d9d02c6
| author | iuc |
|---|---|
| date | Wed, 06 Aug 2025 08:38:24 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:bd267e082f86 |
|---|---|
| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">1.0.2</token> | |
| 3 <token name="@VERSION_SUFFIX@">0</token> | |
| 4 <token name="@LICENSE@">GPL-2.0-or-later</token> | |
| 5 <xml name="requirements"> | |
| 6 <requirements> | |
| 7 <container type="docker">sebimer/samba-v4-qiime2:2024.2</container> | |
| 8 </requirements> | |
| 9 </xml> | |
| 10 <xml name="numb_blanks_arg"> | |
| 11 <param argument="--numb_blanks" type="integer" label="Number of blank samples" value="1" min="0" help="Specifies the number of blanks included in the data set"/> | |
| 12 </xml> | |
| 13 <xml name="numb_ind_arg"> | |
| 14 <param argument="--numb_ind" type="text" label="Number of individuals per group" optional="false" help="A comma-separated vector (e.g. 3,2) indicating the number of individual samples in each group"> | |
| 15 <validator type="regex" message="Enter a comma-separated list of positive integers (e.g., 3,2)">^\d+(,\d+)*$</validator> | |
| 16 </param> | |
| 17 </xml> | |
| 18 <xml name="runs_and_regression_args"> | |
| 19 <param argument="--runs" type="integer" label="Number of runs" value="2" min="1" max="10" help="Specifies the number of times that the function should run the decontamination procedure on the data."/> | |
| 20 <param argument="--regression" type="integer" label="Regression" value="0" min="0" max="2" help="Specifies the regression equation used to calculate the constant. 0 = it chooses between regression 1 and regression 2 based on the lower threshold and upper threshold arguments. 1 = it always uses regression 1. 2 = it always uses regression 2"/> | |
| 21 <param argument="--low_threshold" type="integer" label="Lower threshold" value="40" min="0" help="Selects the lower point for switching between regression 1 and regression 2. It is usually best not to change this value"/> | |
| 22 <param argument="--up_threshold" type="integer" label="Upper threshold" value="400" min="0" help="Selects the higher point for switching between regression 1 and regression 2. It is usually best not to change this value"/> | |
| 23 </xml> | |
| 24 <xml name="thresh_args"> | |
| 25 <param argument="--thresh" type="float" label="Zero proportion threshold" value="0.7" min="0" max="1" help="This is the threshold at which if that proportion of 0s are present for an OTU within a group, all samples will be set to 0 for that OTU for that group"/> | |
| 26 <param argument="--prop_thresh" type="float" label="Proportional threshold" value="0.00005" min="0" max="1" help="This is the threshold at which if the number of reads for a particular OTU are below this proportion, the OTU will be set to zero for all individuals in that group"/> | |
| 27 </xml> | |
| 28 <xml name="citations"> | |
| 29 <citations> | |
| 30 <citation type="doi">10.1002/edn3.11</citation> | |
| 31 </citations> | |
| 32 </xml> | |
| 33 <xml name="creators"> | |
| 34 <creator> | |
| 35 <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053"/> | |
| 36 </creator> | |
| 37 </xml> | |
| 38 </macros> |