--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jan 24 18:37:14 2023 +0000
@@ -0,0 +1,68 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.20.0</token>
+    <token name="@SUFFIX_VERSION@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>
+            <requirement type="package" version="2.2.1">r-argparse</requirement>
+            <requirement type="package" version="1.0.10">r-dplyr</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btz247</citation>
+            <citation type="doi">10.1158/1541-7786.MCR-16-0459</citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+          <xref type="bio.tools">IsoformSwitchAnalyzeR</xref>
+          <xref type="bioconductor">isoformswitchanalyzer</xref>
+        </xrefs>
+    </xml>
+    <xml name="macro_disordered_regions">
+        <param argument="smoothingWindowSize" type="integer" min="1" value="5" label="Smoothing window size" help="An integer indicating how 
+            large a sliding window should be used to calculate a smoothed (via mean) disordered probability score of a particular position in
+            a peptide. This has as a smoothing effect which prevents IDRs from not being detected (or from being split into sub-IDRs) by a 
+            single residue with low probability. The trade off is worse accuracy of detecting the exact edges of the IDRs. To turn it off 
+            smoothing simply set to 1." />
+        <param argument="probabilityCutoff" type="float" min="0" value="0.5" label="Probability cutoff" help="Cutoff applied to the (smoothed) 
+            disordered probability score for calling a residue as disordered. The default, 30 amino acids, is an accepted standard for long IDRs" />
+        <param argument="minIdrSize" type="integer" min="0" value="30" label="Minimum IDR size" help="How long a stretch of disordered amino acid 
+            constitute the region part of the Intrinsically Disordered Region (IDR) definition. The default, 30 amino acids, is an accepted 
+            standard for long IDRs" />
+    </xml>
+    <xml name="macro_alpha_difcutoff">
+        <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 
+            than for calling significant switches." />
+        <param argument="dIFcutoff" type="float" min="0" max="1" value="0.1" label="dIFcutoff" help="The cutoff which the changes in (absolute) isoform usage 
+            must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed 
+            significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential
+            expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%)" />
+    </xml>
+    <xml name="macro_ifcutoff" token_value="" token_help="">
+        <param argument="IFcutoff" type="float" min="0" max="1" value="@VALUE@" label="IFcutoff" help="@HELP@" />
+    </xml>
+    <xml name="macro_onlysigisoforms1">
+        <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential 
+            used isoforms" help="This parameter indicates whether both isoforms the pairs considered if reduceFurtherToGenesWithConsequenshould be significantly 
+            differential used (as indicated by the alpha and dIFcutoff parameters). Default is disabled (aka only one of the isoforms in a pair should be
+            significantly differential used)" />
+    </xml>
+    <xml name="macro_onlysigisoforms2">
+        <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential 
+            used isoforms" help="This parameter indicates whether to only consider significant isoforms, meaning only analyzing genes where at least two isoforms 
+            which both have significant usage changes in opposite direction (quite strict). Naturally this only works if the isoform switch test used have isoform 
+            resolution (which the build in *isoformSwitchTestDEXSeq* has). If disabled all isoforms with an absolute dIF value larger than dIFcutoff in a gene with 
+            significant switches (defined by alpha and dIFcutoff) are included in the pairwise comparison" />
+    </xml>
+    <xml name="macro_keeisoforminall" token_checked="">
+        <param argument="keepIsoformInAllConditions" type="boolean" truevalue="--keepIsoformInAllConditions" falsevalue="" checked="@CHECKED@" label="Keep isoforms in all conditions" 
+            help="This parameter indicates whether an isoform should be kept in all comparisons even if it is only deemed significant (as defined by the 
+            alpha and dIFcutoff parameters) in one comparison" />
+    </xml>
+    <xml name="macro_onlyswitching">
+        <param argument="onlySwitchingGenes" type="boolean" truevalue="--onlySwitchingGenes" falsevalue="" checked="true" label="Only switching genes" help="Only 
+            analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters)" />
+    </xml>
+</macros>
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