Mercurial > repos > iuc > rgrnastar
comparison rg_rnaStar.xml @ 20:91e0f03268ca draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
| author | iuc |
|---|---|
| date | Wed, 08 Sep 2021 14:35:09 +0000 |
| parents | 44959aa06aeb |
| children | 980d2a2e1180 |
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| 19:44959aa06aeb | 20:91e0f03268ca |
|---|---|
| 50 #for $sj_input in $twopass.sj_precalculated: | 50 #for $sj_input in $twopass.sj_precalculated: |
| 51 '$sj_input' | 51 '$sj_input' |
| 52 #end for | 52 #end for |
| 53 #if str($twopass.twopassMode) != 'None': | 53 #if str($twopass.twopassMode) != 'None': |
| 54 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': | 54 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': |
| 55 #if not $refGenomeSource.GTFconditional.sjdbGTFfile: | 55 ## need to check first if its a cached index or from history |
| 56 ## case of cached index without built-in gene model, | 56 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided |
| 57 ## when user does not supply the optional gtf, but | 57 #if str($refGenomeSource.geneSource) == 'history': |
| 58 ## specifies the splice junction overhang | 58 #if not $refGenomeSource.GTFconditional.sjdbGTFfile: |
| 59 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang | 59 ## case of cached index without built-in gene model, |
| 60 ## when user does not supply the optional gtf, but | |
| 61 ## specifies the splice junction overhang | |
| 62 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang | |
| 63 #end if | |
| 60 #end if | 64 #end if |
| 61 #end if | 65 #end if |
| 62 #end if | 66 #end if |
| 63 | 67 |
| 64 --quantMode ${quantmode_output.quantMode} | 68 --quantMode ${quantmode_output.quantMode} |
| 832 | 836 |
| 833 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> | 837 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> |
| 834 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> | 838 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> |
| 835 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> | 839 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> |
| 836 </test> | 840 </test> |
| 841 <!-- test Basic twopass with a built-in gtf index option --> | |
| 842 <test expect_num_outputs="3"> | |
| 843 <conditional name="singlePaired"> | |
| 844 <param name="sPaired" value="single" /> | |
| 845 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> | |
| 846 </conditional> | |
| 847 <conditional name="refGenomeSource"> | |
| 848 <param name="geneSource" value="indexed" /> | |
| 849 <conditional name="GTFconditional"> | |
| 850 <param name="GTFselect" value="with-gtf" /> | |
| 851 <param name="genomeDir" value="001" /> | |
| 852 </conditional> | |
| 853 </conditional> | |
| 854 <conditional name="twopass"> | |
| 855 <param name="twopassMode" value="Basic" /> | |
| 856 </conditional> | |
| 857 <section name="oformat"> | |
| 858 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> | |
| 859 <param name="outSAMmapqUnique" value="255" /> | |
| 860 </section> | |
| 861 <section name="filter"> | |
| 862 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> | |
| 863 <conditional name="output_params2"> | |
| 864 <param name="output_select2" value="yes" /> | |
| 865 </conditional> | |
| 866 </section> | |
| 867 <section name="algo"> | |
| 868 <conditional name="params"> | |
| 869 <param name="settingsType" value="full" /> | |
| 870 </conditional> | |
| 871 </section> | |
| 872 | |
| 873 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> | |
| 874 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> | |
| 875 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> | |
| 876 </test> | |
| 837 <!-- test "multisample" twopass --> | 877 <!-- test "multisample" twopass --> |
| 838 <test expect_num_outputs="3"> | 878 <test expect_num_outputs="3"> |
| 839 <conditional name="singlePaired"> | 879 <conditional name="singlePaired"> |
| 840 <param name="sPaired" value="single" /> | 880 <param name="sPaired" value="single" /> |
| 841 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> | 881 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |