Mercurial > repos > iuc > rgrnastar
comparison rg_rnaStar.xml @ 18:c772497b2c32 draft
"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 |
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| 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 |