# HG changeset patch
# User artbio
# Date 1522794435 14400
# Node ID 6aba6cca3fab207cee2c218d255cf4133fbf362c
# Parent  cf60c3338279aea8bb5773c98200e5ec54ba8ed1
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5

diff -r cf60c3338279 -r 6aba6cca3fab macros.xml
--- a/macros.xml	Sun Apr 01 18:10:44 2018 -0400
+++ b/macros.xml	Tue Apr 03 18:27:15 2018 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
   <macros>
-    <token name="@WRAPPER_VERSION@">0.5.1</token>
+    <token name="@WRAPPER_VERSION@">0.5.4</token>
     <xml name="rsem_options">
         <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)">
         </param>
diff -r cf60c3338279 -r 6aba6cca3fab rsem-bwt2.xml
--- a/rsem-bwt2.xml	Sun Apr 01 18:10:44 2018 -0400
+++ b/rsem-bwt2.xml	Tue Apr 03 18:27:15 2018 -0400
@@ -46,15 +46,15 @@
       &&
     #end if
     
-    #if $run_rsem.select == "Yes":
+    #if $run_rsem.select == "Yes" and $run_rsem.input.format == 'fastq':
       ## uncompress fastq.gz or fastqsanger.gz if needed
-      #if $run_rsem.input.fastq.matepair=="single":
+      #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single":
         #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
           gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
         #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
           ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
         #end if
-      #elif $run_rsem.input.fastq.matepair=="paired":
+      #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
         #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 &&
@@ -141,16 +141,6 @@
           $run_rsem.input.fasta.fasta1
           $run_rsem.input.fasta.fasta2
         #end if
-      #elif $run_rsem.input.format=="sam"
-        #if $run_rsem.input.matepair=="paired":
-          --paired-end
-        #end if
-        #if $run_rsem.input.rsem_sam._extension == 'sam':
-          --sam
-        #elif $run_rsem.input.rsem_sam._extension == 'bam':
-          --bam
-        #end if
-        $run_rsem.input.rsem_sam
       #end if
       ## RSEM reference
       #if $run_rsem.reference.refSrc == 'history':
@@ -250,7 +240,6 @@
           <param name="format" type="select" label="RSEM Input file type">
             <option value="fastq">FASTQ</option>
             <option value="fasta">FASTA</option>
-            <option value="sam">SAM/BAM</option>
           </param>
           <when value="fastq">
             <param name="fastq_select" size="15" type="select" label="FASTQ type" >
@@ -289,14 +278,6 @@
             </conditional>
             <expand macro="bowtie2_options"/>
           </when>
-          <when value="sam">
-              <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
-              <param name="matepair" type="select" label="Library Type">
-                <option value="single">Single End Reads</option>
-                <option value="paired">Paired End Reads</option>
-              </param>
-              <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
-          </when>
         </conditional>
         <expand macro="rsem_options"/>
         <conditional name="rsem_outputs">
diff -r cf60c3338279 -r 6aba6cca3fab rsem.xml
--- a/rsem.xml	Sun Apr 01 18:10:44 2018 -0400
+++ b/rsem.xml	Tue Apr 03 18:27:15 2018 -0400
@@ -48,13 +48,13 @@
     
     #if $run_rsem.select == "Yes":
       ## uncompress fastq.gz or fastqsanger.gz if needed
-      #if $run_rsem.input.fastq.matepair=="single":
+      #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single":
         #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
           gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
         #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
           ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
         #end if
-      #elif $run_rsem.input.fastq.matepair=="paired":
+      #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
         #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 &&
@@ -148,16 +148,6 @@
           $run_rsem.input.fasta.fasta1
           $run_rsem.input.fasta.fasta2
         #end if
-      #elif $run_rsem.input.format=="sam"
-        #if $run_rsem.input.matepair=="paired":
-          --paired-end
-        #end if
-        #if $run_rsem.input.rsem_sam._extension == 'sam':
-          --sam
-        #elif $run_rsem.input.rsem_sam._extension == 'bam':
-          --bam
-        #end if
-        $run_rsem.input.rsem_sam
       #end if
       ## RSEM reference
       #if $run_rsem.reference.refSrc == 'history':
@@ -257,7 +247,6 @@
           <param name="format" type="select" label="RSEM Input file type">
             <option value="fastq">FASTQ</option>
             <option value="fasta">FASTA</option>
-            <option value="sam">SAM/BAM</option>
           </param>
           <when value="fastq">
             <param name="fastq_select" size="15" type="select" label="FASTQ type" >
@@ -296,14 +285,6 @@
             </conditional>
             <expand macro="bowtie_options"/>
           </when>
-          <when value="sam">
-              <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
-              <param name="matepair" type="select" label="Library Type">
-                <option value="single">Single End Reads</option>
-                <option value="paired">Paired End Reads</option>
-              </param>
-              <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
-          </when>
         </conditional>
         <expand macro="rsem_options"/>
         <conditional name="rsem_outputs">