Mercurial > repos > iuc > rgrnastar
comparison rg_rnaStar.xml @ 28:3e94726bfa9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
author | iuc |
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date | Sun, 11 Feb 2024 00:01:54 +0000 |
parents | 79de45b5069b |
children | 4014de1b6daf |
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27:79de45b5069b | 28:3e94726bfa9d |
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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. |