Mercurial > repos > iuc > isoformswitchanalyzer
changeset 4:512d6462f2ce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
| author | iuc |
|---|---|
| date | Tue, 30 May 2023 08:39:23 +0000 |
| parents | 02a77166b29a |
| children | b3f292d9f35d |
| files | IsoformSwitchAnalyzeR.R isoformswitchanalyzer.xml macros.xml |
| diffstat | 3 files changed, 78 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- 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$isoformFeatures, + file = "IsoformFeatures.tsv", + quote = FALSE, + sep = "\t", + col.names = TRUE, + row.names = FALSE + ) ### Volcano like plot: outputFile <- file.path(getwd(), "volcanoPlot.pdf")
--- a/isoformswitchanalyzer.xml Wed May 24 13:33:53 2023 +0000 +++ b/isoformswitchanalyzer.xml Tue May 30 08:39:23 2023 +0000 @@ -238,7 +238,7 @@ label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when doing transcript assembly (unassigned transcripts and merged genes)" /> <conditional name="novoisoforms"> - <param name="selector" type="select" label="Analsys mode"> + <param name="selector" type="select" label="Analysis mode"> <option value="novel">Include novel isoforms in analysis</option> <option value="reference">Reference-only analysis</option> </param> @@ -577,6 +577,18 @@ <filter>functionMode['selector'] == 'second_step'</filter> <filter>functionMode['analysis_mode']['selector'] == 'top'</filter> </data> + <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${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">
--- 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>