Mercurial > repos > artbio > rsem

diff rsem-bwt2.xml @ 11:c86ed39b72eb draft

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"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 10719ebe96c608be124360a4be62ec4d164412b3"
author artbio
date Sun, 05 Jan 2020 22:07:36 +0000
parents 6aba6cca3fab
children
line wrap: on
line diff
--- a/rsem-bwt2.xml	Tue Apr 03 18:27:15 2018 -0400
+++ b/rsem-bwt2.xml	Sun Jan 05 22:07:36 2020 +0000
@@ -3,10 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-  <requirements>
-    <requirement type="package" version="1.3.0">rsem</requirement>
-    <requirement type="package" version="2.3.4">bowtie2</requirement>
-  </requirements>
+    <expand macro="requirements" />
     <stdio>
         <exit_code range="1:" level="warning" description="Tool exception" />
     </stdio>
@@ -24,8 +21,6 @@
         #if $job.polya.polya_length:
           --polyA-length $job.polya.polya_length
         #end if
-      #elif $job.polya.polya_use == 'none':
-        --no-polyA
       #end if
       $job.ntog
       #if $job.transcript_to_gene_map:
@@ -58,7 +53,7 @@
         #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
@@ -163,7 +158,7 @@
       </param>
       <when value="index">
         <conditional name="self_reference">
-          <param name="ref_type" type="select" label="Reference transcript source">
+          <param name="ref_type" type="select" label="Reference source">
             <option value="transcripts">transcript fasta</option>
             <option value="genomic">reference genome and gtf</option>
           </param>
@@ -228,7 +223,7 @@
         <conditional name="reference">
           <param name="refSrc" type="select" label="RSEM Reference Source">
             <option value="history">From your history</option>
-            <option value="self">Prepare RSEM Reference with this tool</option>
+            <option value="self">RSEM Reference prepared with this tool</option>
           </param>
           <when value="history">
             <param name="rsem_ref" type="data" format="rsem_bt2_ref" label="RSEM reference" />
@@ -326,23 +321,23 @@
    <test>
       <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="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
+      <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
+      <param name="reference_name" value="ebola_genome"/>
       <param name="select" value="Yes"/>
-      <param name="sample" value="rsem_sample"/>
+      <param name="sample" value="ebola_RNAseq"/>
       <param name="refSrc" value="self"/>
       <param name="format" value="fastq"/>
       <param name="matepair" value="single"/>
-      <param name="singlefastq" value="test.fq" ftype="fastqsanger"/>
+      <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/>
       <param name="result_bams" value="none"/>
       <output name="reference_file">
         <assert_contents>
-          <has_text text="ref" />
+          <has_text text="ebola_genome" />
         </assert_contents>
       </output>
-      <output name="gene_abundances" value="gene_abundances.tab2"/> 
-      <output name="isoform_abundances" value="isoform_abundances.tab2" /> 
+      <output name="gene_abundances" value="refgen_gene_abundances.bt2.tab"/> 
+      <output name="isoform_abundances" value="refgen_isoform_abundances.bt2.tab" /> 
       <output name="log"> 
         <assert_contents>
           <has_text text="Expression Results are written" />
@@ -350,25 +345,84 @@
       </output>
     </test>
     <test>
+      <!-- test paired end on ebola genome -->
       <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="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
+      <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
+      <param name="reference_name" value="ebola"/>
+      <param name="select" value="Yes"/>
+      <param name="sample" value="ebola_RNAseq"/>
+      <param name="refSrc" value="self"/>
+      <param name="format" value="fastq"/>
+      <param name="matepair" value="paired"/>
+      <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
+      <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
+      <param name="result_bams" value="both"/>
+      <output name="reference_file">
+        <assert_contents>
+          <has_text text="ebola" />
+        </assert_contents>
+      </output>
+      <output name="gene_abundances" value="paired_refgen_gene_abundances.bt2.tab"/>
+      <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt2.tab" />
+      <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt2.bam" ftype="bam" lines_diff="4" />
+      <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt2.bam" ftype="bam" lines_diff="4" />
+      <output name="log">
+        <assert_contents>
+          <has_text text="Expression Results are written" />
+        </assert_contents>
+      </output>
+    </test>
+     <test>
+      <!-- test paired end on ebola transcripts -->
+      <param name="select_job" value="index"/>
+      <param name="ref_type" value="transcripts"/>
+      <param name="reference_fasta_file" value="Ebola_transcripts.fa" ftype="fasta"/>
+      <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="gtf"/>
+      <param name="reference_name" value="ebola"/>
+      <param name="select" value="Yes"/>
+      <param name="sample" value="ebola_RNAseq"/>
+      <param name="refSrc" value="self"/>
+      <param name="format" value="fastq"/>
+      <param name="matepair" value="paired"/>
+      <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger.gz"/>
+      <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
+      <param name="result_bams" value="default"/>
+      <output name="reference_file">
+        <assert_contents>
+          <has_text text="ebola" />
+        </assert_contents>
+      </output>
+      <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt2.tab"/>
+      <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt2.tab" />
+      <output name="transcript_sorted_bam" value="paired_reftrans_transcripts.bt2.bam" ftype="bam" lines_diff="2" />
+      <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"/>
+      <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
+      <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
+      <param name="reference_name" value="ebola"/>
       <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="single"/>
-      <param name="singlefastq" value="test.fastq.gz" ftype="fastqsanger.gz"/>
+      <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
       <param name="result_bams" value="none"/>
       <output name="reference_file">
         <assert_contents>
-          <has_text text="ref" />
+          <has_text text="ebola" />
         </assert_contents>
       </output>
-      <output name="gene_abundances" value="gene_abundances.tab2"/>
-      <output name="isoform_abundances" value="isoform_abundances.tab2" />
+      <output name="gene_abundances" value="single_refgen_gene_abundances.bt2.tab"/>
+      <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt2.tab" />
       <output name="log">
         <assert_contents>
           <has_text text="Expression Results are written" />
@@ -378,26 +432,13 @@
     <test>
       <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="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
+      <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
+      <param name="reference_name" value="alone"/>
       <param name="select" value="No"/>
       <output name="reference_file">
         <assert_contents>
-          <has_text text="ref" />
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <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="No"/>
-      <output name="reference_file">
-        <assert_contents>
-          <has_text text="ref" />
+          <has_text text="alone" />
         </assert_contents>
       </output>
     </test>