# HG changeset patch
# User bgruening
# Date 1492085893 14400
# Node ID 979bff04ae7d2f38695211a864ab0acd5c6780b8
# Parent  0b689bf9473c074de7c1c36a618081d2986e46ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243

diff -r 0b689bf9473c -r 979bff04ae7d salmon.xml
--- a/salmon.xml	Thu Feb 02 19:37:14 2017 -0500
+++ b/salmon.xml	Thu Apr 13 08:18:13 2017 -0400
@@ -13,6 +13,7 @@
     </macros>
 
     <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="0.7.2">salmon</requirement>
     </requirements>
 
@@ -45,10 +46,16 @@
             #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 &&
@@ -56,6 +63,11 @@
             #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 &&
@@ -68,10 +80,24 @@
             --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 ./output
@@ -168,12 +194,12 @@
                 <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>
@@ -333,6 +359,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test> <!-- gzipped input -->
+            <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 name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="single_or_paired_opts" value="paired" />
             <param name="input_mate1" value="reads_1.fastq" />
diff -r 0b689bf9473c -r 979bff04ae7d test-data/reads_1.fastq.gz
Binary file test-data/reads_1.fastq.gz has changed
diff -r 0b689bf9473c -r 979bff04ae7d test-data/reads_2.fastq.gz
Binary file test-data/reads_2.fastq.gz has changed