Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 18:c772497b2c32 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
author iuc
date Mon, 15 Mar 2021 13:46:07 +0000
parents e132e7d02a3e
children 44959aa06aeb
comparison
equal deleted inserted replaced
17:7ed2edc1337f 18:c772497b2c32
865 865
866 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> 866 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
867 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> 867 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
868 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> 868 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
869 </test> 869 </test>
870 </tests> 870 <!-- test "genomeSAindexNbases" parameter -->
871 <test expect_num_outputs="3">
872 <conditional name="singlePaired">
873 <param name="sPaired" value="single" />
874 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
875 </conditional>
876 <conditional name="refGenomeSource">
877 <param name="geneSource" value="history" />
878 <param name="genomeFastaFiles" value="tophat_test.fa" />
879 <param name="genomeSAindexNbases" value="14" />
880 </conditional>
881 <section name="oformat">
882 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
883 <param name="outSAMmapqUnique" value="255" />
884 </section>
885 <section name="algo">
886 <conditional name="params">
887 <param name="settingsType" value="default" />
888 </conditional>
889 </section>
890 <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" />
891 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/>
892 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" />
893 </test>
894 <test expect_num_outputs="3">
895 <conditional name="singlePaired">
896 <param name="sPaired" value="single" />
897 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
898 </conditional>
899 <conditional name="refGenomeSource">
900 <param name="geneSource" value="history" />
901 <param name="genomeFastaFiles" value="tophat_test.fa" />
902 <param name="genomeSAindexNbases" value="10" />
903 </conditional>
904 <section name="oformat">
905 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
906 <param name="outSAMmapqUnique" value="255" />
907 </section>
908 <section name="algo">
909 <conditional name="params">
910 <param name="settingsType" value="default" />
911 </conditional>
912 </section>
913 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" />
914 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/>
915 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" />
916 </test>
917 </tests>
871 <help><![CDATA[ 918 <help><![CDATA[
872 **What it does** 919 **What it does**
873 920
874 STAR_ is an ultrafast universal RNA-seq aligner. 921 STAR_ is an ultrafast universal RNA-seq aligner.
875 922