Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 28:3e94726bfa9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
author iuc
date Sun, 11 Feb 2024 00:01:54 +0000
parents 79de45b5069b
children 4014de1b6daf
comparison
equal deleted inserted replaced
27:79de45b5069b 28:3e94726bfa9d
88 ## Read FLAG 88 ## Read FLAG
89 --outSAMprimaryFlag ${oformat.outSAMprimaryFlag} 89 --outSAMprimaryFlag ${oformat.outSAMprimaryFlag}
90 90
91 ## Read MAPQ 91 ## Read MAPQ
92 --outSAMmapqUnique ${oformat.outSAMmapqUnique} 92 --outSAMmapqUnique ${oformat.outSAMmapqUnique}
93
94 ## Transform diploid mode output to reference coordinates
95 #if str($refGenomeSource.geneSource) == 'history':
96 #if 'diploidconditional' in $refGenomeSource:
97 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
98 '${refGenomeSource.diploidconditional.genomeTransformOutput}'
99 #end if
100 #end if
101 #end if
93 102
94 ## Output filter parameters 103 ## Output filter parameters
95 104
96 ## Basic Filters 105 ## Basic Filters
97 #if str($filter.basic_filters) != 'None': 106 #if str($filter.basic_filters) != 'None':
314 <expand macro="SJDBOPTIONS"/> 323 <expand macro="SJDBOPTIONS"/>
315 <expand macro="quantMode" /> 324 <expand macro="quantMode" />
316 </when> 325 </when>
317 <when value="without-gtf"> 326 <when value="without-gtf">
318 <expand macro="quantModeNoGTF" /> 327 <expand macro="quantModeNoGTF" />
328 </when>
329 </conditional>
330 <conditional name="diploidconditional">
331 <param name="diploid" type="select" label="Diploid mode" help="Map RNA-seq reads to a diploid genome">
332 <option value="No" selected="True">No</option>
333 <option value="Yes">Yes</option>
334 </param>
335 <when value="Yes">
336 <param argument="--genomeTransformVCF" type="data" format="vcf" label="VCF file with diploid SNVs and InDels" help="The homozygous and heterozygous alleles from this VCF will be inserted into the reference genome to create a transformed genome with two haplotypes"/>
337 <param argument="--genomeTransformOutput" type="boolean" checked="false" truevalue="--genomeTransformOutput SAM SJ Quant" falsevalue="--genomeTransformOutput None" label="Transform alignments, spliced junctions and quantifications back to the reference coordinates" help="Use this if downstream processing relies on reference coordinates"/>
338 </when>
339 <when value="No">
319 </when> 340 </when>
320 </conditional> 341 </conditional>
321 </when> 342 </when>
322 </conditional> 343 </conditional>
323 344
808 </conditional> 829 </conditional>
809 </section> 830 </section>
810 831
811 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/> 832 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
812 </test> 833 </test>
834 <!-- test 10 -->
813 <test expect_num_outputs="3"> 835 <test expect_num_outputs="3">
814 <conditional name="singlePaired"> 836 <conditional name="singlePaired">
815 <param name="sPaired" value="single" /> 837 <param name="sPaired" value="single" />
816 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 838 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
817 </conditional> 839 </conditional>
835 </conditional> 857 </conditional>
836 </section> 858 </section>
837 859
838 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> 860 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
839 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 861 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
840 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 862 <output name="mapped_reads" file="rnastar_test_mapped_reads_test10.bam" compare="sim_size" delta="634" />
841 </test> 863 </test>
842 <!-- twopass mode tests --> 864 <!-- twopass mode tests -->
843 <!-- test Basic twopass --> 865 <!-- test Basic twopass -->
844 <test expect_num_outputs="3"> 866 <test expect_num_outputs="3">
845 <conditional name="singlePaired"> 867 <conditional name="singlePaired">
1115 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> 1137 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
1116 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> 1138 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
1117 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> 1139 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
1118 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> 1140 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
1119 </test> 1141 </test>
1142 <!-- test diploid mode -->
1143 <test expect_num_outputs="3">
1144 <conditional name="singlePaired">
1145 <param name="sPaired" value="single" />
1146 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
1147 </conditional>
1148 <conditional name="refGenomeSource">
1149 <param name="geneSource" value="history" />
1150 <param name="genomeFastaFiles" value="tophat_test.fa.gz" />
1151 <param name="genomeSAindexNbases" value="5" />
1152 </conditional>
1153 <conditional name="diploidconditional">
1154 <param name="diploid" value="Yes" />
1155 <!-- generated from rnastar_test_mapped_reads.bam with
1156 bcftools mpileup and bcftools call -->
1157 <param name="genomeTransformVCF" value="rnastar_test_mapped_reads.vcf" ftype="vcf" />
1158 <param name="genomeTransformOutput" value="true" />
1159 </conditional>
1160 <output name="output_log" file="rnastar_test_diploid.log" compare="re_match_multiline" />
1161 <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/>
1162 <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" />
1163 </test>
1120 </tests> 1164 </tests>
1121 <help><![CDATA[ 1165 <help><![CDATA[
1122 **What it does** 1166 **What it does**
1123 1167
1124 STAR_ is an ultrafast universal RNA-seq aligner. 1168 STAR_ is an ultrafast universal RNA-seq aligner.