# HG changeset patch
# User bgruening
# Date 1492086000 14400
# Node ID 5bc9cd008ceb515c08312e0a44c81f264e521037
# Parent  1b4ed566a41c06face1be50fcaabb7751c90383b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 359ddec398e18d3e2a534239b1202691595d1243

diff -r 1b4ed566a41c -r 5bc9cd008ceb sailfish.tar.bz2
Binary file sailfish.tar.bz2 has changed
diff -r 1b4ed566a41c -r 5bc9cd008ceb sailfish.xml
--- a/sailfish.xml	Wed Nov 02 10:30:36 2016 -0400
+++ b/sailfish.xml	Thu Apr 13 08:20:00 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="sailfish" name="Sailfish" version="0.10.1">
+<tool id="sailfish" name="Sailfish" version="0.10.1.1">
     <description>transcript quantification from RNA-seq data</description>
     <macros>
         <xml name="strandedness">
@@ -10,6 +10,7 @@
         </xml>
     </macros>
     <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="0.10.1">sailfish</requirement>
     </requirements>
     <stdio>
@@ -33,10 +34,16 @@
             #set $index_path = $refTranscriptSource.index.fields.path
         #end if
         &&
+        #set compressed = 'no'
         #if $single_or_paired.single_or_paired_opts == 'single':
             #if $single_or_paired.input_singles.ext == 'fasta':
                 #set $ext = 'fasta'
             #else:
+                #if $single_or_paired.input_singles.is_of_type("fastq.gz"):
+                    #set compressed = 'GZ'
+                #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"):
+                    #set compressed = 'BZ2'
+                #end if
                 #set $ext = 'fastq'
             #end if
             ln -s $single_or_paired.input_singles ./single.$ext &&
@@ -44,6 +51,11 @@
             #if $single_or_paired.input_mate1.ext == 'fasta':
                 #set $ext = 'fasta'
             #else:
+                #if $single_or_paired.input_mate1.is_of_type("fastq.gz"):
+                    #set compressed = 'GZ'
+                #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"):
+                    #set compressed = 'BZ2'
+                #end if
                 #set $ext = 'fastq'
             #end if
             ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
@@ -56,10 +68,24 @@
             --index $index_path
             #if $single_or_paired.single_or_paired_opts == 'single':
                 --libType ${single_or_paired.strandedness}
-                --unmatedReads ./single.$ext
+                #if $compressed == 'GZ':
+                    --unmatedReads <(zcat ./single.$ext)
+                #else if $compressed == 'BZ2':
+                    --unmatedReads <(bzcat ./single.$ext)
+                #else:
+                    --unmatedReads ./single.$ext
+                #end if
             #else:
-                --mates1 ./mate1.$ext
-                --mates2 ./mate2.$ext
+                #if $compressed == 'GZ':
+                    --mates1 <(zcat ./mate1.$ext)
+                    --mates2 <(zcat ./mate2.$ext)
+                #else if $compressed == 'BZ2':
+                    --mates1 <(bzcat ./mate1.$ext)
+                    --mates2 <(bzcat ./mate2.$ext)
+                #else:
+                    --mates1 ./mate1.$ext
+                    --mates2 ./mate2.$ext
+                #end if
                 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
             #end if
             --output ./results
@@ -138,12 +164,12 @@
                 <option value="paired">Paired-end</option>
             </param>
             <when value="single">
-                <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
+                <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." />
                 <expand macro="strandedness" />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
-                <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
+                <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." />
                 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
                     <option value="M">Mates are oriented in the same direction (M = matching)</option>
                     <option value="O">Mates are oriented away from each other (O = outward)</option>
@@ -273,6 +299,15 @@
             <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
             <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
         </test>
+        <test> <!-- gzipped version of above -->
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="biasCorrect" value="False" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
+        </test>
         <test>
             <param name="single_or_paired_opts" value="paired" />
             <param name="input_mate1" value="reads_1.fastq" />
diff -r 1b4ed566a41c -r 5bc9cd008ceb test-data/reads_1.fastq.gz
Binary file test-data/reads_1.fastq.gz has changed
diff -r 1b4ed566a41c -r 5bc9cd008ceb test-data/reads_2.fastq.gz
Binary file test-data/reads_2.fastq.gz has changed