Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 20:91e0f03268ca draft

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"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
comparison
equal deleted inserted replaced
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" />