Mercurial > repos > iuc > isoformswitchanalyzer
comparison isoformswitchanalyzer.xml @ 2:db30020fee5b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
| author | iuc |
|---|---|
| date | Wed, 24 May 2023 06:06:36 +0000 |
| parents | 5ae218cee629 |
| children | 8575def9219d |
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| 1:5ae218cee629 | 2:db30020fee5b |
|---|---|
| 40 mkdir -p "count_files/factor1/" && | 40 mkdir -p "count_files/factor1/" && |
| 41 mkdir -p "count_files/factor2/" && | 41 mkdir -p "count_files/factor2/" && |
| 42 #end if | 42 #end if |
| 43 #if $functionMode.tool_source.selector == 'stringtie' | 43 #if $functionMode.tool_source.selector == 'stringtie' |
| 44 #set $filename = 't_data.ctab' | 44 #set $filename = 't_data.ctab' |
| 45 #if $functionMode.tool_source.novoisoforms.selector == 'novel' | |
| 46 #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"): | |
| 47 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' && | |
| 48 #set $stringtie_annotation = './stringtie_annotation.gtf.gz' | |
| 49 #else | |
| 50 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' && | |
| 51 #set $stringtie_annotation = './stringtie_annotation.gtf' | |
| 52 #end if | |
| 53 #end if | |
| 45 #else | 54 #else |
| 46 #set $filename = 'quant.sf' | 55 #set $filename = 'quant.sf' |
| 47 #end if | 56 #end if |
| 48 | 57 |
| 49 #for $index in range(len($functionMode.first_factor.trans_counts)): | 58 #for $index in range(len($functionMode.first_factor.trans_counts)): |
| 59 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R' | 68 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R' |
| 60 --modeSelector $functionMode.selector | 69 --modeSelector $functionMode.selector |
| 61 --parentDir './input_files' | 70 --parentDir './input_files' |
| 62 --annotation $annotation | 71 --annotation $annotation |
| 63 --transcriptome $transcriptome | 72 --transcriptome $transcriptome |
| 73 $functionMode.removeNonConvensionalChr | |
| 64 --toolSource $functionMode.tool_source.selector | 74 --toolSource $functionMode.tool_source.selector |
| 65 #if $functionMode.tool_source.selector == 'stringtie' | 75 #if $functionMode.tool_source.selector == 'stringtie' |
| 76 #if $functionMode.tool_source.novoisoforms.selector == 'novel' | |
| 77 --stringtieAnnotation $stringtie_annotation | |
| 78 #end if | |
| 66 --readLength $functionMode.tool_source.averageSize | 79 --readLength $functionMode.tool_source.averageSize |
| 67 $functionMode.tool_source.fixStringTieAnnotationProblem | 80 $functionMode.tool_source.fixStringTieAnnotationProblem |
| 68 #end if | 81 #end if |
| 69 --countFiles $functionMode.countFiles | 82 --countFiles $functionMode.countFiles |
| 70 #else if $functionMode.selector == 'first_step' | 83 #else if $functionMode.selector == 'first_step' |
| 222 <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data | 235 <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data |
| 223 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" /> |
| 224 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" | 237 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" |
| 225 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 |
| 226 doing transcript assembly (unassigned transcripts and merged genes)" /> | 239 doing transcript assembly (unassigned transcripts and merged genes)" /> |
| 240 <conditional name="novoisoforms"> | |
| 241 <param name="selector" type="select" label="Analsys mode"> | |
| 242 <option value="novel">Include novel isoforms in analysis</option> | |
| 243 <option value="reference">Reference-only analysis</option> | |
| 244 </param> | |
| 245 <when value="novel"> | |
| 246 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge" | |
| 247 help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." /> | |
| 248 </when> | |
| 249 <when value="reference"/> | |
| 250 </conditional> | |
| 227 </when> | 251 </when> |
| 228 </conditional> | 252 </conditional> |
| 229 <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation (GTF)" | 253 <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation" |
| 230 help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." /> | 254 help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." /> |
| 231 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome" | 255 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome" |
| 232 help="Please note this different from a fasta file with the sequences of the entire genome." /> | 256 help="Please note this different from a fasta file with the sequences of the entire genome." /> |
| 257 <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false" | |
| 258 label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." /> | |
| 233 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation | 259 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation |
| 234 problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format)."> | 260 problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format)."> |
| 235 <option value="disabled">Disabled</option> | 261 <option value="disabled">Disabled</option> |
| 236 <option value="collection">Collection of count files</option> | 262 <option value="collection">Collection of count files</option> |
| 237 <option value="matrix">Expression matrix</option> | 263 <option value="matrix">Expression matrix</option> |
| 238 </param> | 264 </param> |
| 265 | |
| 239 </when> | 266 </when> |
| 240 | 267 |
| 241 <!--WRAPPER FIRST STEP SECTION--> | 268 <!--WRAPPER FIRST STEP SECTION--> |
| 242 | 269 |
| 243 <when value="first_step"> | 270 <when value="first_step"> |