Mercurial > repos > iuc > isoformswitchanalyzer
comparison macros.xml @ 0:f3fefb6d8254 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
| author | iuc |
|---|---|
| date | Tue, 24 Jan 2023 18:37:14 +0000 |
| parents | |
| children | 2c4e879a81cf |
comparison
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| -1:000000000000 | 0:f3fefb6d8254 |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">1.20.0</token> | |
| 3 <token name="@SUFFIX_VERSION@">0</token> | |
| 4 <xml name="requirements"> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement> | |
| 7 <requirement type="package" version="2.2.1">r-argparse</requirement> | |
| 8 <requirement type="package" version="1.0.10">r-dplyr</requirement> | |
| 9 </requirements> | |
| 10 </xml> | |
| 11 <xml name="citations"> | |
| 12 <citations> | |
| 13 <citation type="doi">10.1093/bioinformatics/btz247</citation> | |
| 14 <citation type="doi">10.1158/1541-7786.MCR-16-0459</citation> | |
| 15 </citations> | |
| 16 </xml> | |
| 17 <xml name="xrefs"> | |
| 18 <xrefs> | |
| 19 <xref type="bio.tools">IsoformSwitchAnalyzeR</xref> | |
| 20 <xref type="bioconductor">isoformswitchanalyzer</xref> | |
| 21 </xrefs> | |
| 22 </xml> | |
| 23 <xml name="macro_disordered_regions"> | |
| 24 <param argument="smoothingWindowSize" type="integer" min="1" value="5" label="Smoothing window size" help="An integer indicating how | |
| 25 large a sliding window should be used to calculate a smoothed (via mean) disordered probability score of a particular position in | |
| 26 a peptide. This has as a smoothing effect which prevents IDRs from not being detected (or from being split into sub-IDRs) by a | |
| 27 single residue with low probability. The trade off is worse accuracy of detecting the exact edges of the IDRs. To turn it off | |
| 28 smoothing simply set to 1." /> | |
| 29 <param argument="probabilityCutoff" type="float" min="0" value="0.5" label="Probability cutoff" help="Cutoff applied to the (smoothed) | |
| 30 disordered probability score for calling a residue as disordered. The default, 30 amino acids, is an accepted standard for long IDRs" /> | |
| 31 <param argument="minIdrSize" type="integer" min="0" value="30" label="Minimum IDR size" help="How long a stretch of disordered amino acid | |
| 32 constitute the region part of the Intrinsically Disordered Region (IDR) definition. The default, 30 amino acids, is an accepted | |
| 33 standard for long IDRs" /> | |
| 34 </xml> | |
| 35 <xml name="macro_alpha_difcutoff"> | |
| 36 <param argument="alpha" type="float" min="0" max="1" value="0.05" label="Alpha value" help="The cutoff which the FDR correct p-values must be smaller | |
| 37 than for calling significant switches." /> | |
| 38 <param argument="dIFcutoff" type="float" min="0" max="1" value="0.1" label="dIFcutoff" help="The cutoff which the changes in (absolute) isoform usage | |
| 39 must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed | |
| 40 significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential | |
| 41 expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%)" /> | |
| 42 </xml> | |
| 43 <xml name="macro_ifcutoff" token_value="" token_help=""> | |
| 44 <param argument="IFcutoff" type="float" min="0" max="1" value="@VALUE@" label="IFcutoff" help="@HELP@" /> | |
| 45 </xml> | |
| 46 <xml name="macro_onlysigisoforms1"> | |
| 47 <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential | |
| 48 used isoforms" help="This parameter indicates whether both isoforms the pairs considered if reduceFurtherToGenesWithConsequenshould be significantly | |
| 49 differential used (as indicated by the alpha and dIFcutoff parameters). Default is disabled (aka only one of the isoforms in a pair should be | |
| 50 significantly differential used)" /> | |
| 51 </xml> | |
| 52 <xml name="macro_onlysigisoforms2"> | |
| 53 <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential | |
| 54 used isoforms" help="This parameter indicates whether to only consider significant isoforms, meaning only analyzing genes where at least two isoforms | |
| 55 which both have significant usage changes in opposite direction (quite strict). Naturally this only works if the isoform switch test used have isoform | |
| 56 resolution (which the build in *isoformSwitchTestDEXSeq* has). If disabled all isoforms with an absolute dIF value larger than dIFcutoff in a gene with | |
| 57 significant switches (defined by alpha and dIFcutoff) are included in the pairwise comparison" /> | |
| 58 </xml> | |
| 59 <xml name="macro_keeisoforminall" token_checked=""> | |
| 60 <param argument="keepIsoformInAllConditions" type="boolean" truevalue="--keepIsoformInAllConditions" falsevalue="" checked="@CHECKED@" label="Keep isoforms in all conditions" | |
| 61 help="This parameter indicates whether an isoform should be kept in all comparisons even if it is only deemed significant (as defined by the | |
| 62 alpha and dIFcutoff parameters) in one comparison" /> | |
| 63 </xml> | |
| 64 <xml name="macro_onlyswitching"> | |
| 65 <param argument="onlySwitchingGenes" type="boolean" truevalue="--onlySwitchingGenes" falsevalue="" checked="true" label="Only switching genes" help="Only | |
| 66 analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters)" /> | |
| 67 </xml> | |
| 68 </macros> |