Mercurial > repos > iuc > isoformswitchanalyzer

annotate macros.xml @ 0:bb611fa3bc3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
author iuc
date Tue, 24 Jan 2023 18:36:55 +0000
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children 5ae218cee629
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bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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1 <macros>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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2 <token name="@TOOL_VERSION@">1.20.0</token>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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3 <token name="@SUFFIX_VERSION@">0</token>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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4 <xml name="requirements">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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5 <requirements>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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6 <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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7 <requirement type="package" version="2.2.1">r-argparse</requirement>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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8 <requirement type="package" version="1.0.10">r-dplyr</requirement>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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9 </requirements>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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10 </xml>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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11 <xml name="citations">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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12 <citations>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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13 <citation type="doi">10.1093/bioinformatics/btz247</citation>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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14 <citation type="doi">10.1158/1541-7786.MCR-16-0459</citation>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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15 </citations>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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16 </xml>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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17 <xml name="xrefs">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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18 <xrefs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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19 <xref type="bio.tools">IsoformSwitchAnalyzeR</xref>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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20 <xref type="bioconductor">isoformswitchanalyzer</xref>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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21 </xrefs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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22 </xml>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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23 <xml name="macro_disordered_regions">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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24 <param argument="smoothingWindowSize" type="integer" min="1" value="5" label="Smoothing window size" help="An integer indicating how
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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25 large a sliding window should be used to calculate a smoothed (via mean) disordered probability score of a particular position in
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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27 single residue with low probability. The trade off is worse accuracy of detecting the exact edges of the IDRs. To turn it off
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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28 smoothing simply set to 1." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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29 <param argument="probabilityCutoff" type="float" min="0" value="0.5" label="Probability cutoff" help="Cutoff applied to the (smoothed)
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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30 disordered probability score for calling a residue as disordered. The default, 30 amino acids, is an accepted standard for long IDRs" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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31 <param argument="minIdrSize" type="integer" min="0" value="30" label="Minimum IDR size" help="How long a stretch of disordered amino acid
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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32 constitute the region part of the Intrinsically Disordered Region (IDR) definition. The default, 30 amino acids, is an accepted
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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33 standard for long IDRs" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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34 </xml>
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35 <xml name="macro_alpha_difcutoff">
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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37 than for calling significant switches." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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41 expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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42 </xml>
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43 <xml name="macro_ifcutoff" token_value="" token_help="">
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44 <param argument="IFcutoff" type="float" min="0" max="1" value="@VALUE@" label="IFcutoff" help="@HELP@" />
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45 </xml>
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46 <xml name="macro_onlysigisoforms1">
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47 <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential
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48 used isoforms" help="This parameter indicates whether both isoforms the pairs considered if reduceFurtherToGenesWithConsequenshould be significantly
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
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50 significantly differential used)" />
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51 </xml>
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52 <xml name="macro_onlysigisoforms2">
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53 <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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54 used isoforms" help="This parameter indicates whether to only consider significant isoforms, meaning only analyzing genes where at least two isoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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55 which both have significant usage changes in opposite direction (quite strict). Naturally this only works if the isoform switch test used have isoform
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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56 resolution (which the build in *isoformSwitchTestDEXSeq* has). If disabled all isoforms with an absolute dIF value larger than dIFcutoff in a gene with
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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57 significant switches (defined by alpha and dIFcutoff) are included in the pairwise comparison" />
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58 </xml>
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59 <xml name="macro_keeisoforminall" token_checked="">
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60 <param argument="keepIsoformInAllConditions" type="boolean" truevalue="--keepIsoformInAllConditions" falsevalue="" checked="@CHECKED@" label="Keep isoforms in all conditions"
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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
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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62 alpha and dIFcutoff parameters) in one comparison" />
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63 </xml>
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64 <xml name="macro_onlyswitching">
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65 <param argument="onlySwitchingGenes" type="boolean" truevalue="--onlySwitchingGenes" falsevalue="" checked="true" label="Only switching genes" help="Only
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66 analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters)" />
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67 </xml>
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68 </macros>