# HG changeset patch
# User iuc
# Date 1685435963 0
# Node ID 512d6462f2ce23886aacec7b89f9b2809127aeb9
# Parent  02a77166b29a976534848c3f0a9859d0793c45b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3

diff -r 02a77166b29a -r 512d6462f2ce IsoformSwitchAnalyzeR.R
--- a/IsoformSwitchAnalyzeR.R	Wed May 24 13:33:53 2023 +0000
+++ b/IsoformSwitchAnalyzeR.R	Tue May 30 08:39:23 2023 +0000
@@ -893,6 +893,32 @@
       row.names = FALSE
     )
 
+    write.table(
+      SwitchList$switchConsequence,
+      file = "switchConsequence_fulldata.tsv",
+      quote = FALSE,
+      sep = "\t",
+      col.names = TRUE,
+      row.names = FALSE
+    )
+
+    write.table(
+      SwitchList$AlternativeSplicingAnalysis,
+      file = "switchSplicing_fulldata.tsv",
+      quote = FALSE,
+      sep = "\t",
+      col.names = TRUE,
+      row.names = FALSE
+    )
+
+    write.table(
+      SwitchList$isoformFeatures,
+      file = "IsoformFeatures.tsv",
+      quote = FALSE,
+      sep = "\t",
+      col.names = TRUE,
+      row.names = FALSE
+    )
 
     ### Volcano like plot:
     outputFile <- file.path(getwd(), "volcanoPlot.pdf")
diff -r 02a77166b29a -r 512d6462f2ce isoformswitchanalyzer.xml
--- a/isoformswitchanalyzer.xml	Wed May 24 13:33:53 2023 +0000
+++ b/isoformswitchanalyzer.xml	Tue May 30 08:39:23 2023 +0000
@@ -238,7 +238,7 @@
                             label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when 
                                 doing transcript assembly (unassigned transcripts and merged genes)" />
                         <conditional name="novoisoforms">
-                            <param name="selector" type="select" label="Analsys mode">
+                            <param name="selector" type="select" label="Analysis mode">
                                 <option value="novel">Include novel isoforms in analysis</option>
                                 <option value="reference">Reference-only analysis</option>
                             </param>
@@ -577,6 +577,18 @@
             <filter>functionMode['selector'] == 'second_step'</filter>
             <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
         </data>
+        <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${tool.name} on ${on_string}: alternative splicing full data">
+            <filter>functionMode['selector'] == 'second_step'</filter>
+            <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
+        </data>
+        <data name="consequences_fulldata" format="tabular" from_work_dir="switchConsequence_fulldata.tsv" label="${tool.name} on ${on_string}: funcional consequences full data">
+            <filter>functionMode['selector'] == 'second_step'</filter>
+            <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
+        </data>
+        <data name="isoformFeatures" format="tabular" from_work_dir="IsoformFeatures.tsv" label="${tool.name} on ${on_string}: isoform features">
+            <filter>functionMode['selector'] == 'second_step'</filter>
+            <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
+        </data>
         <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${tool.name} on ${on_string}: single gene analysis">
             <filter>functionMode['selector'] == 'second_step'</filter>
             <filter>functionMode['analysis_mode']['selector'] == 'single'</filter>
@@ -739,7 +751,7 @@
             </output>        
         </test>
         <!--Test 06: generate plots and summaries full analsys-->
-        <test expect_num_outputs="9">
+        <test expect_num_outputs="12">
             <conditional name="functionMode">
                 <param name="selector" value="second_step"/>
                 <param name="robject" value="test04.RData"/>
@@ -841,9 +853,27 @@
             <output name="consequencesEnrichment" file="test06_consequences_enrichment.tabular" ftype="tabular" lines_diff="4"/>
             <output name="splicingSummary" file="test06_splicing_summary.tabular" ftype="tabular" lines_diff="4"/>
             <output name="splicingEnrichment" file="test06_splicing_enrichment.tabular" ftype="tabular" lines_diff="4"/>
+            <output name="consequences_fulldata" ftype="tabular">
+                <assert_contents>
+                    <has_size value="51508" delta="100"/>
+                    <has_text text="ORF_genomic"/>
+                </assert_contents>
+            </output>
+            <output name="splicing_fulldata" ftype="tabular">
+                <assert_contents>
+                    <has_size value="46951" delta="100"/>
+                    <has_text text="ATTS_genomic_start"/>
+                </assert_contents>
+            </output>
+            <output name="isoformFeatures" ftype="tabular">
+                <assert_contents>
+                    <has_size value="95185" delta="100"/>
+                    <has_text text="gene_overall_mean"/>
+                </assert_contents>
+            </output>
         </test>
         <!--Test 07: generate plots and summaries full analsys all inputs-->
-        <test expect_num_outputs="9">
+        <test expect_num_outputs="12">
             <conditional name="functionMode">
                 <param name="selector" value="second_step"/>
                 <param name="robject" value="test04.RData"/>
@@ -995,6 +1025,24 @@
                     <has_text text="A5 gain (paired with A5 loss)"/>
                 </assert_contents>
             </output>
+            <output name="consequences_fulldata" ftype="tabular">
+                <assert_contents>
+                    <has_size value="103581" delta="50"/>
+                    <has_text text="signal_peptide_identified"/>
+                </assert_contents>
+            </output>
+            <output name="splicing_fulldata" ftype="tabular">
+                <assert_contents>
+                    <has_size value="46951" delta="50"/>
+                    <has_text text="ATTS_genomic_start"/>
+                </assert_contents>
+            </output>
+            <output name="isoformFeatures" ftype="tabular">
+                <assert_contents>
+                    <has_size value="99607" delta="50"/>
+                    <has_text text="gene_overall_mean"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test 08: analyze single gene-->
         <test expect_num_outputs="2">
diff -r 02a77166b29a -r 512d6462f2ce macros.xml
--- a/macros.xml	Wed May 24 13:33:53 2023 +0000
+++ b/macros.xml	Tue May 30 08:39:23 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.20.0</token>
-    <token name="@SUFFIX_VERSION@">3</token>
+    <token name="@SUFFIX_VERSION@">4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>