Mercurial > repos > artbio > rsem

diff rsem.xml @ 4:1823c8e07d96 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f
author artbio
date Fri, 01 Jun 2018 03:00:34 -0400
parents 26ead8419b63
children 835a2f3372b5
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line diff
--- a/rsem.xml	Tue Apr 03 18:25:39 2018 -0400
+++ b/rsem.xml	Fri Jun 01 03:00:34 2018 -0400
@@ -58,7 +58,7 @@
         #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
           gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
           gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
-        #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
+        #elif $run_rsem.input.fastq.fastq1.is_of_type('fastq') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'):
           ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
           ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
         #end if
@@ -356,6 +356,34 @@
         </assert_contents>
       </output>
     </test>
+   <test>
+      <!-- test fastqsanger paired end -->
+      <param name="select_job" value="index"/>
+      <param name="ref_type" value="genomic"/>
+      <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
+      <param name="gtf" value="ref.gtf" ftype="gtf"/>
+      <param name="reference_name" value="ref"/>
+      <param name="select" value="Yes"/>
+      <param name="sample" value="rsem_sample"/>
+      <param name="refSrc" value="self"/>
+      <param name="format" value="fastq"/>
+      <param name="matepair" value="paired"/>
+      <param name="fastq1" value="test2_forward.fastq" ftype="fastqsanger"/>
+      <param name="fastq2" value="test2_reverse.fastq" ftype="fastqsanger"/>
+      <param name="result_bams" value="none" />
+      <output name="reference_file">
+        <assert_contents>
+          <has_text text="ref" />
+        </assert_contents>
+      </output>
+      <output name="gene_abundances" value="de_gene_abundances.tab"/> 
+      <output name="isoform_abundances" value="de_isoform_abundances.tab" /> 
+      <output name="log"> 
+        <assert_contents>
+          <has_text text="Expression Results are written" />
+        </assert_contents>
+      </output>
+    </test>
     <test>
       <param name="select_job" value="index"/>
       <param name="ref_type" value="genomic"/>