Mercurial > repos > iuc > rgrnastar

diff 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
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line diff
--- 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>
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