Mercurial > repos > iuc > isoformswitchanalyzer

comparison isoformswitchanalyzer.xml @ 7:d3377a16d881 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
author iuc
date Wed, 14 Jan 2026 09:30:42 +0000
parents b3f292d9f35d
children
comparison
equal deleted inserted replaced
6:298d81e5e138 7:d3377a16d881
58 #set $filename = 'quant.sf' 58 #set $filename = 'quant.sf'
59 #else 59 #else
60 #set $filename = 'abundance.tsv' 60 #set $filename = 'abundance.tsv'
61 #end if 61 #end if
62 62
63 ## read cofactor repeats and generate cofactor_map dictionary
64 ## cofactor_map structure: {file_path: {cofactor_name: cofactor_level_name, ...}, ...}
65 #set $cofactor_map = {}
66 #set $cofactor_names = []
67 #for $cofactor_item in $functionMode.tool_source.cofactor:
68 #set $cofactor_name = str($cofactor_item.cofactor_name)
69 $cofactor_names.append($cofactor_name)
70 #for $level_item in $cofactor_item.cofactor_level:
71 #set $level_name = str($level_item.cofactor_level_name)
72 #for $level_file in $level_item.cofactor_level_files:
73 #set $file_path = str($level_file)
74 #if $file_path not in $cofactor_map:
75 #set $cofactor_map[$file_path] = {}
76 #end if
77 #set $cofactor_map[$file_path][$cofactor_name] = $level_name
78 #end for
79 #end for
80 #end for
81
82 ## create file_to_sample_map dictionary
83 #set $file_to_sample_map = {}
84
63 #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)): 85 #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):
86 #set $sampleID = str($functionMode.tool_source.first_factor.factorLevel) + str($index)
87 #set $trans_file = $functionMode.tool_source.first_factor.trans_counts[$index]
88 #set $file_to_sample_map[$sampleID] = str($trans_file)
64 $conditions.append($functionMode.tool_source.first_factor.factorLevel) 89 $conditions.append($functionMode.tool_source.first_factor.factorLevel)
65 $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index)) 90 $sampleIDs.append($sampleID)
66 $replicates.append($index) 91 $replicates.append($index)
67 mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' && 92 mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' &&
68 ln -s $functionMode.tool_source.first_factor.trans_counts[$index] './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' && 93 ln -s $trans_file './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' &&
69 #end for 94 #end for
70 95
71 #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)): 96 #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):
97 #set $sampleID = str($functionMode.tool_source.second_factor.factorLevel) + str($index)
98 #set $trans_file = $functionMode.tool_source.second_factor.trans_counts[$index]
99 #set $file_to_sample_map[$sampleID] = str($trans_file)
72 $conditions.append($functionMode.tool_source.second_factor.factorLevel) 100 $conditions.append($functionMode.tool_source.second_factor.factorLevel)
73 $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index)) 101 $sampleIDs.append($sampleID)
74 $replicates.append($index) 102 $replicates.append($index)
75 mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' && 103 mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' &&
76 ln -s $functionMode.tool_source.second_factor.trans_counts[$index] './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' && 104 ln -s $trans_file './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' &&
77 #end for 105 #end for
78 106
107
79 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R' 108 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
80 #for $i, $condition in enumerate($conditions) 109 #for $i, $condition in enumerate($conditions)
81 --condition $condition 110 --condition $condition
82 --sampleID $sampleIDs[$i] 111 --sampleID $sampleIDs[$i]
83 --replicate $replicates[$i] 112 --replicate $replicates[$i]
113 #set $sample_file = $file_to_sample_map[$sampleIDs[$i]]
114 #if $sample_file in $cofactor_map
115 #set $cofactor_values = []
116 #for $cofactor_name in $cofactor_names:
117 #if $cofactor_name in $cofactor_map[$sample_file]
118 #set $cofactor_value = $cofactor_map[$sample_file][$cofactor_name]
119 #silent $cofactor_values.append(str($cofactor_value))
120 #end if
121 #end for
122 --cofactors $(','.join($cofactor_values))
123 #end if
84 #end for 124 #end for
125 #if len($cofactor_names) > 0
126 --cofactorNames $(','.join($cofactor_names))
127 #end if
85 $functionMode.pairedSamples 128 $functionMode.pairedSamples
86 --modeSelector $functionMode.selector 129 --modeSelector $functionMode.selector
87 --parentDir './input_files' 130 --parentDir './input_files'
88 --annotation $annotation 131 --annotation $annotation
89 --transcriptome $transcriptome 132 --transcriptome $transcriptome
646 <assert_contents> 689 <assert_contents>
647 <has_size value="652170" delta="300"/> 690 <has_size value="652170" delta="300"/>
648 </assert_contents> 691 </assert_contents>
649 </output> 692 </output>
650 <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/> 693 <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/>
651 <output name="sample_annotation" file="test02_samples_annotation.tabular" ftype="tabular"/> 694 <output name="sample_annotation">
695 <assert_contents>
696 <has_text_matching expression="sampleID\s+condition"/>
697 <has_text_matching expression="health0\s+health"/>
698 <has_text_matching expression="health1\s+health"/>
699 <has_text_matching expression="cancer0\s+cancer"/>
700 <has_text_matching expression="cancer1\s+cancer"/>
701 </assert_contents>
702 </output>
652 </test> 703 </test>
653 <!-- Test 03: Data import mode generate collection count files--> 704 <!-- Test 03: Data import mode generate collection count files-->
654 <test expect_num_outputs="3"> 705 <test expect_num_outputs="3">
655 <conditional name="functionMode"> 706 <conditional name="functionMode">
656 <param name="selector" value="data_import"/> 707 <param name="selector" value="data_import"/>
1113 <output name="switchList" ftype="rdata"> 1164 <output name="switchList" ftype="rdata">
1114 <assert_contents> 1165 <assert_contents>
1115 <has_size value="652170" delta="300"/> 1166 <has_size value="652170" delta="300"/>
1116 </assert_contents> 1167 </assert_contents>
1117 </output> 1168 </output>
1118 <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/> 1169 <output name="sample_annotation">
1170 <assert_contents>
1171 <has_text_matching expression="sampleID\s+condition\s+replicate"/>
1172 <has_text_matching expression="health0\s+health\s+0"/>
1173 <has_text_matching expression="health1\s+health\s+1"/>
1174 <has_text_matching expression="cancer0\s+cancer\s+0"/>
1175 <has_text_matching expression="cancer1\s+cancer\s+1"/>
1176 </assert_contents>
1177 </output>
1178 </test>
1179 <!-- Test 11: Data import mode add cofactor-->
1180 <test expect_num_outputs="3">
1181 <conditional name="functionMode">
1182 <param name="selector" value="data_import"/>
1183 <param name="genomeAnnotation" value="gencode.hg19.chr10_1000.gtf.gz"/>
1184 <param name="transcriptome" value="transcriptome_stringtie.fasta.gz"/>
1185 <param name="countFiles" value="matrix"/>
1186 <conditional name="tool_source">
1187 <param name="selector" value="stringtie"/>
1188 <conditional name="novoisoforms">
1189 <param name="selector" value="novel"/>
1190 <param name="stringtieAnnotation" value="annotation_stringtie.gtf.gz"/>
1191 </conditional>
1192 <section name="first_factor">
1193 <param name="factorLevel" value="EWS-FLI1"/>
1194 <param name="trans_counts" value="ASP14_1.tabular,ASP14_2.tabular,ASP14_3.tabular"/>
1195 </section>
1196 <section name="second_factor">
1197 <param name="factorLevel" value="no-EWS-FLI1"/>
1198 <param name="trans_counts" value="ASP14_doxycycline_1.tabular,ASP14_doxycycline_2.tabular,ASP14_doxycycline_3.tabular"/>
1199 </section>
1200 <repeat name="cofactor">
1201 <param name="cofactor_name" value="Batch"/>
1202 <repeat name="cofactor_level">
1203 <param name="cofactor_level_name" value="batch1"/>
1204 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular"/>
1205 </repeat>
1206 <repeat name="cofactor_level">
1207 <param name="cofactor_level_name" value="batch2"/>
1208 <param name="cofactor_level_files" value="ASP14_2.tabular,ASP14_doxycycline_2.tabular"/>
1209 </repeat>
1210 <repeat name="cofactor_level">
1211 <param name="cofactor_level_name" value="batch3"/>
1212 <param name="cofactor_level_files" value="ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
1213 </repeat>
1214 </repeat>
1215 <repeat name="cofactor">
1216 <param name="cofactor_name" value="Age"/>
1217 <repeat name="cofactor_level">
1218 <param name="cofactor_level_name" value="20"/>
1219 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular,ASP14_2.tabular"/>
1220 </repeat>
1221 <repeat name="cofactor_level">
1222 <param name="cofactor_level_name" value="60"/>
1223 <param name="cofactor_level_files" value="ASP14_doxycycline_2.tabular,ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
1224 </repeat>
1225 </repeat>
1226 </conditional>
1227 </conditional>
1228 <output name="switchList" ftype="rdata">
1229 <assert_contents>
1230 <has_size value="374542" delta="300"/>
1231 </assert_contents>
1232 </output>
1233 <output name="matrix_counts" file="stringtie_counts.tabular" ftype="tabular" lines_diff="6"/>
1234 <output name="sample_annotation">
1235 <assert_contents>
1236 <has_text_matching expression="sampleID\s+condition\s+Batch\s+Age"/>
1237 <has_text_matching expression="EWSXFLI10\s+EWSXFLI1\s+batch1\s+20"/>
1238 <has_text_matching expression="EWSXFLI11\s+EWSXFLI1\s+batch2\s+20"/>
1239 <has_text_matching expression="EWSXFLI12\s+EWSXFLI1\s+batch3\s+60"/>
1240 <has_text_matching expression="noXEWSXFLI10\s+noXEWSXFLI1\s+batch1\s+20"/>
1241 <has_text_matching expression="noXEWSXFLI11\s+noXEWSXFLI1\s+batch2\s+60"/>
1242 <has_text_matching expression="noXEWSXFLI12\s+noXEWSXFLI1\s+batch3\s+60"/>
1243 </assert_contents>
1244 </output>
1119 </test> 1245 </test>
1120 </tests> 1246 </tests>
1121 <help><![CDATA[ 1247 <help><![CDATA[
1122 1248
1123 .. class:: infomark 1249 .. class:: infomark