Mercurial > repos > iuc > isoformswitchanalyzer

comparison isoformswitchanalyzer.xml @ 4:8575def9219d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
author iuc
date Tue, 30 May 2023 08:39:02 +0000
parents db30020fee5b
children 69fa05891f9d
comparison
equal deleted inserted replaced
3:bc68526d0e69 4:8575def9219d
236 quantified is 75 bp paired ends the the user should supply readLength=75" /> 236 quantified is 75 bp paired ends the the user should supply readLength=75" />
237 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" 237 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true"
238 label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when 238 label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when
239 doing transcript assembly (unassigned transcripts and merged genes)" /> 239 doing transcript assembly (unassigned transcripts and merged genes)" />
240 <conditional name="novoisoforms"> 240 <conditional name="novoisoforms">
241 <param name="selector" type="select" label="Analsys mode"> 241 <param name="selector" type="select" label="Analysis mode">
242 <option value="novel">Include novel isoforms in analysis</option> 242 <option value="novel">Include novel isoforms in analysis</option>
243 <option value="reference">Reference-only analysis</option> 243 <option value="reference">Reference-only analysis</option>
244 </param> 244 </param>
245 <when value="novel"> 245 <when value="novel">
246 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge" 246 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge"
575 </data> 575 </data>
576 <data name="splicingEnrichment" format="tabular" from_work_dir="splicingEnrichment.tsv" label="${tool.name} on ${on_string}: splicing enrichment"> 576 <data name="splicingEnrichment" format="tabular" from_work_dir="splicingEnrichment.tsv" label="${tool.name} on ${on_string}: splicing enrichment">
577 <filter>functionMode['selector'] == 'second_step'</filter> 577 <filter>functionMode['selector'] == 'second_step'</filter>
578 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter> 578 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
579 </data> 579 </data>
580 <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${tool.name} on ${on_string}: alternative splicing full data">
581 <filter>functionMode['selector'] == 'second_step'</filter>
582 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
583 </data>
584 <data name="consequences_fulldata" format="tabular" from_work_dir="switchConsequence_fulldata.tsv" label="${tool.name} on ${on_string}: funcional consequences full data">
585 <filter>functionMode['selector'] == 'second_step'</filter>
586 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
587 </data>
588 <data name="isoformFeatures" format="tabular" from_work_dir="IsoformFeatures.tsv" label="${tool.name} on ${on_string}: isoform features">
589 <filter>functionMode['selector'] == 'second_step'</filter>
590 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
591 </data>
580 <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${tool.name} on ${on_string}: single gene analysis"> 592 <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${tool.name} on ${on_string}: single gene analysis">
581 <filter>functionMode['selector'] == 'second_step'</filter> 593 <filter>functionMode['selector'] == 'second_step'</filter>
582 <filter>functionMode['analysis_mode']['selector'] == 'single'</filter> 594 <filter>functionMode['analysis_mode']['selector'] == 'single'</filter>
583 </data> 595 </data>
584 </outputs> 596 </outputs>
737 <has_size value="500518" delta="300"/> 749 <has_size value="500518" delta="300"/>
738 </assert_contents> 750 </assert_contents>
739 </output> 751 </output>
740 </test> 752 </test>
741 <!--Test 06: generate plots and summaries full analsys--> 753 <!--Test 06: generate plots and summaries full analsys-->
742 <test expect_num_outputs="9"> 754 <test expect_num_outputs="12">
743 <conditional name="functionMode"> 755 <conditional name="functionMode">
744 <param name="selector" value="second_step"/> 756 <param name="selector" value="second_step"/>
745 <param name="robject" value="test04.RData"/> 757 <param name="robject" value="test04.RData"/>
746 <section name="analyzeSwitchConsequences"> 758 <section name="analyzeSwitchConsequences">
747 <param name="ntCutoff" value="50"/> 759 <param name="ntCutoff" value="50"/>
839 <output name="mostSwitching" file="test06_switching.tabular" ftype="tabular" lines_diff="4"/> 851 <output name="mostSwitching" file="test06_switching.tabular" ftype="tabular" lines_diff="4"/>
840 <output name="consequencesSummary" file="test06_consequences_summary.tabular" ftype="tabular" lines_diff="4"/> 852 <output name="consequencesSummary" file="test06_consequences_summary.tabular" ftype="tabular" lines_diff="4"/>
841 <output name="consequencesEnrichment" file="test06_consequences_enrichment.tabular" ftype="tabular" lines_diff="4"/> 853 <output name="consequencesEnrichment" file="test06_consequences_enrichment.tabular" ftype="tabular" lines_diff="4"/>
842 <output name="splicingSummary" file="test06_splicing_summary.tabular" ftype="tabular" lines_diff="4"/> 854 <output name="splicingSummary" file="test06_splicing_summary.tabular" ftype="tabular" lines_diff="4"/>
843 <output name="splicingEnrichment" file="test06_splicing_enrichment.tabular" ftype="tabular" lines_diff="4"/> 855 <output name="splicingEnrichment" file="test06_splicing_enrichment.tabular" ftype="tabular" lines_diff="4"/>
856 <output name="consequences_fulldata" ftype="tabular">
857 <assert_contents>
858 <has_size value="51508" delta="100"/>
859 <has_text text="ORF_genomic"/>
860 </assert_contents>
861 </output>
862 <output name="splicing_fulldata" ftype="tabular">
863 <assert_contents>
864 <has_size value="46951" delta="100"/>
865 <has_text text="ATTS_genomic_start"/>
866 </assert_contents>
867 </output>
868 <output name="isoformFeatures" ftype="tabular">
869 <assert_contents>
870 <has_size value="95185" delta="100"/>
871 <has_text text="gene_overall_mean"/>
872 </assert_contents>
873 </output>
844 </test> 874 </test>
845 <!--Test 07: generate plots and summaries full analsys all inputs--> 875 <!--Test 07: generate plots and summaries full analsys all inputs-->
846 <test expect_num_outputs="9"> 876 <test expect_num_outputs="12">
847 <conditional name="functionMode"> 877 <conditional name="functionMode">
848 <param name="selector" value="second_step"/> 878 <param name="selector" value="second_step"/>
849 <param name="robject" value="test04.RData"/> 879 <param name="robject" value="test04.RData"/>
850 <section name="analyzeSwitchConsequences"> 880 <section name="analyzeSwitchConsequences">
851 <param name="ntCutoff" value="20"/> 881 <param name="ntCutoff" value="20"/>
993 <assert_contents> 1023 <assert_contents>
994 <has_size value="1157" delta="50"/> 1024 <has_size value="1157" delta="50"/>
995 <has_text text="A5 gain (paired with A5 loss)"/> 1025 <has_text text="A5 gain (paired with A5 loss)"/>
996 </assert_contents> 1026 </assert_contents>
997 </output> 1027 </output>
1028 <output name="consequences_fulldata" ftype="tabular">
1029 <assert_contents>
1030 <has_size value="103581" delta="50"/>
1031 <has_text text="signal_peptide_identified"/>
1032 </assert_contents>
1033 </output>
1034 <output name="splicing_fulldata" ftype="tabular">
1035 <assert_contents>
1036 <has_size value="46951" delta="50"/>
1037 <has_text text="ATTS_genomic_start"/>
1038 </assert_contents>
1039 </output>
1040 <output name="isoformFeatures" ftype="tabular">
1041 <assert_contents>
1042 <has_size value="99607" delta="50"/>
1043 <has_text text="gene_overall_mean"/>
1044 </assert_contents>
1045 </output>
998 </test> 1046 </test>
999 <!-- Test 08: analyze single gene--> 1047 <!-- Test 08: analyze single gene-->
1000 <test expect_num_outputs="2"> 1048 <test expect_num_outputs="2">
1001 <conditional name="functionMode"> 1049 <conditional name="functionMode">
1002 <param name="selector" value="second_step"/> 1050 <param name="selector" value="second_step"/>