Mercurial > repos > iuc > rgrnastar
diff 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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--- a/rg_rnaStar.xml Fri Jan 15 17:38:35 2021 +0000 +++ b/rg_rnaStar.xml Mon Mar 15 13:46:07 2021 +0000 @@ -867,7 +867,54 @@ <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> </test> - </tests> + <!-- test "genomeSAindexNbases" parameter --> + <test expect_num_outputs="3"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeSAindexNbases" value="14" /> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + <param name="outSAMmapqUnique" value="255" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" /> + </test> + <test expect_num_outputs="3"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa" /> + <param name="genomeSAindexNbases" value="10" /> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + <param name="outSAMmapqUnique" value="255" /> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="default" /> + </conditional> + </section> + <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" /> + </test> + </tests> <help><![CDATA[ **What it does**