Mercurial > repos > iuc > isoformswitchanalyzer
diff isoformswitchanalyzer.xml @ 6:293ed243039c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
| author | iuc |
|---|---|
| date | Wed, 14 Jan 2026 09:30:17 +0000 |
| parents | 69fa05891f9d |
| children |
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--- a/isoformswitchanalyzer.xml Fri Jun 02 10:26:51 2023 +0000 +++ b/isoformswitchanalyzer.xml Wed Jan 14 09:30:17 2026 +0000 @@ -60,28 +60,71 @@ #set $filename = 'abundance.tsv' #end if + ## read cofactor repeats and generate cofactor_map dictionary + ## cofactor_map structure: {file_path: {cofactor_name: cofactor_level_name, ...}, ...} + #set $cofactor_map = {} + #set $cofactor_names = [] + #for $cofactor_item in $functionMode.tool_source.cofactor: + #set $cofactor_name = str($cofactor_item.cofactor_name) + $cofactor_names.append($cofactor_name) + #for $level_item in $cofactor_item.cofactor_level: + #set $level_name = str($level_item.cofactor_level_name) + #for $level_file in $level_item.cofactor_level_files: + #set $file_path = str($level_file) + #if $file_path not in $cofactor_map: + #set $cofactor_map[$file_path] = {} + #end if + #set $cofactor_map[$file_path][$cofactor_name] = $level_name + #end for + #end for + #end for + + ## create file_to_sample_map dictionary + #set $file_to_sample_map = {} + #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)): + #set $sampleID = str($functionMode.tool_source.first_factor.factorLevel) + str($index) + #set $trans_file = $functionMode.tool_source.first_factor.trans_counts[$index] + #set $file_to_sample_map[$sampleID] = str($trans_file) $conditions.append($functionMode.tool_source.first_factor.factorLevel) - $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index)) + $sampleIDs.append($sampleID) $replicates.append($index) mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' && - ln -s $functionMode.tool_source.first_factor.trans_counts[$index] './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' && + ln -s $trans_file './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' && #end for #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)): + #set $sampleID = str($functionMode.tool_source.second_factor.factorLevel) + str($index) + #set $trans_file = $functionMode.tool_source.second_factor.trans_counts[$index] + #set $file_to_sample_map[$sampleID] = str($trans_file) $conditions.append($functionMode.tool_source.second_factor.factorLevel) - $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index)) + $sampleIDs.append($sampleID) $replicates.append($index) mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' && - ln -s $functionMode.tool_source.second_factor.trans_counts[$index] './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' && + ln -s $trans_file './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' && #end for + Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R' #for $i, $condition in enumerate($conditions) --condition $condition --sampleID $sampleIDs[$i] --replicate $replicates[$i] + #set $sample_file = $file_to_sample_map[$sampleIDs[$i]] + #if $sample_file in $cofactor_map + #set $cofactor_values = [] + #for $cofactor_name in $cofactor_names: + #if $cofactor_name in $cofactor_map[$sample_file] + #set $cofactor_value = $cofactor_map[$sample_file][$cofactor_name] + #silent $cofactor_values.append(str($cofactor_value)) + #end if + #end for + --cofactors $(','.join($cofactor_values)) + #end if #end for + #if len($cofactor_names) > 0 + --cofactorNames $(','.join($cofactor_names)) + #end if $functionMode.pairedSamples --modeSelector $functionMode.selector --parentDir './input_files' @@ -648,7 +691,15 @@ </assert_contents> </output> <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/> - <output name="sample_annotation" file="test02_samples_annotation.tabular" ftype="tabular"/> + <output name="sample_annotation"> + <assert_contents> + <has_text_matching expression="sampleID\s+condition"/> + <has_text_matching expression="health0\s+health"/> + <has_text_matching expression="health1\s+health"/> + <has_text_matching expression="cancer0\s+cancer"/> + <has_text_matching expression="cancer1\s+cancer"/> + </assert_contents> + </output> </test> <!-- Test 03: Data import mode generate collection count files--> <test expect_num_outputs="3"> @@ -1115,7 +1166,82 @@ <has_size value="652170" delta="300"/> </assert_contents> </output> - <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/> + <output name="sample_annotation"> + <assert_contents> + <has_text_matching expression="sampleID\s+condition\s+replicate"/> + <has_text_matching expression="health0\s+health\s+0"/> + <has_text_matching expression="health1\s+health\s+1"/> + <has_text_matching expression="cancer0\s+cancer\s+0"/> + <has_text_matching expression="cancer1\s+cancer\s+1"/> + </assert_contents> + </output> + </test> + <!-- Test 11: Data import mode add cofactor--> + <test expect_num_outputs="3"> + <conditional name="functionMode"> + <param name="selector" value="data_import"/> + <param name="genomeAnnotation" value="gencode.hg19.chr10_1000.gtf.gz"/> + <param name="transcriptome" value="transcriptome_stringtie.fasta.gz"/> + <param name="countFiles" value="matrix"/> + <conditional name="tool_source"> + <param name="selector" value="stringtie"/> + <conditional name="novoisoforms"> + <param name="selector" value="novel"/> + <param name="stringtieAnnotation" value="annotation_stringtie.gtf.gz"/> + </conditional> + <section name="first_factor"> + <param name="factorLevel" value="EWS-FLI1"/> + <param name="trans_counts" value="ASP14_1.tabular,ASP14_2.tabular,ASP14_3.tabular"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="no-EWS-FLI1"/> + <param name="trans_counts" value="ASP14_doxycycline_1.tabular,ASP14_doxycycline_2.tabular,ASP14_doxycycline_3.tabular"/> + </section> + <repeat name="cofactor"> + <param name="cofactor_name" value="Batch"/> + <repeat name="cofactor_level"> + <param name="cofactor_level_name" value="batch1"/> + <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular"/> + </repeat> + <repeat name="cofactor_level"> + <param name="cofactor_level_name" value="batch2"/> + <param name="cofactor_level_files" value="ASP14_2.tabular,ASP14_doxycycline_2.tabular"/> + </repeat> + <repeat name="cofactor_level"> + <param name="cofactor_level_name" value="batch3"/> + <param name="cofactor_level_files" value="ASP14_3.tabular,ASP14_doxycycline_3.tabular"/> + </repeat> + </repeat> + <repeat name="cofactor"> + <param name="cofactor_name" value="Age"/> + <repeat name="cofactor_level"> + <param name="cofactor_level_name" value="20"/> + <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular,ASP14_2.tabular"/> + </repeat> + <repeat name="cofactor_level"> + <param name="cofactor_level_name" value="60"/> + <param name="cofactor_level_files" value="ASP14_doxycycline_2.tabular,ASP14_3.tabular,ASP14_doxycycline_3.tabular"/> + </repeat> + </repeat> + </conditional> + </conditional> + <output name="switchList" ftype="rdata"> + <assert_contents> + <has_size value="374542" delta="300"/> + </assert_contents> + </output> + <output name="matrix_counts" file="stringtie_counts.tabular" ftype="tabular" lines_diff="6"/> + <output name="sample_annotation"> + <assert_contents> + <has_text_matching expression="sampleID\s+condition\s+Batch\s+Age"/> + <has_text_matching expression="EWSXFLI10\s+EWSXFLI1\s+batch1\s+20"/> + <has_text_matching expression="EWSXFLI11\s+EWSXFLI1\s+batch2\s+20"/> + <has_text_matching expression="EWSXFLI12\s+EWSXFLI1\s+batch3\s+60"/> + <has_text_matching expression="noXEWSXFLI10\s+noXEWSXFLI1\s+batch1\s+20"/> + <has_text_matching expression="noXEWSXFLI11\s+noXEWSXFLI1\s+batch2\s+60"/> + <has_text_matching expression="noXEWSXFLI12\s+noXEWSXFLI1\s+batch3\s+60"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[