# HG changeset patch
# User iuc
# Date 1616190510 0
# Node ID 893655fa55f9a32063f881fc96a8c44ca8dc6b81
# Parent  56162e4460048a97487d76e7c397f9cfd61f4d57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"

diff -r 56162e446004 -r 893655fa55f9 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Feb 11 12:18:36 2020 -0500
+++ b/align_and_estimate_abundance.xml	Fri Mar 19 21:48:30 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@">
+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1">
     <description>on a de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -20,15 +20,20 @@
             #if $inputs.left_input.is_of_type('fasta'):
                 ln -s '$inputs.left_input' paired_left.fa &&
                 ln -s '$inputs.right_input' paired_right.fa
-            #else:
+            #else if $inputs.left_input.is_of_type('fastqsanger'):
                 ln -s '$inputs.left_input' paired_left.fq &&
                 ln -s '$inputs.right_input' paired_right.fq
+            #else:
+                ln -s '$inputs.left_input' paired_left.fq.gz &&
+                ln -s '$inputs.right_input' paired_right.fq.gz
             #end if
         #else:
             #if $inputs.input.is_of_type('fasta'):
                 ln -s '$inputs.input' single.fa
+            #else if $inputs.input.is_of_type('fastqsanger'):
+                ln -s '$inputs.input' single.fq
             #else:
-                ln -s '$inputs.input' single.fq
+                ln -s '$inputs.input' single.fq.gz
             #end if
         #end if
 
@@ -47,8 +52,10 @@
 
             #if $inputs.left_input.is_of_type('fasta'):
                 --left paired_left.fa --right paired_right.fa --seqType fa
+            #else if $inputs.left_input.is_of_type('fastqsanger'):
+                --left paired_left.fq --right paired_right.fq --seqType fq
             #else:
-                --left paired_left.fq --right paired_right.fq --seqType fq
+                --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq
             #end if
 
             #if $inputs.strand.is_strand_specific:
@@ -60,8 +67,10 @@
         #else:
             #if $inputs.input.is_of_type('fasta'):
                 --single single.fa --seqType fa
+            #else if $inputs.input.is_of_type('fastqsanger'):
+                --single single.fq --seqType fq
             #else:
-                --single single.fq --seqType fq
+                --single single.fq.gz --seqType fq
             #end if
 
             #if $inputs.strand.is_strand_specific:
@@ -87,8 +96,8 @@
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
+                <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -103,7 +112,7 @@
                 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
             </when>
             <when value="single">
-                <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -177,8 +186,8 @@
     <tests>
         <test>
             <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
+            <param name="left_input" value="reads.left.fq.gz"/>
+            <param name="right_input" value="reads.right.fq.gz"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
             <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
diff -r 56162e446004 -r 893655fa55f9 test-data/reads.left.fq.gz
Binary file test-data/reads.left.fq.gz has changed
diff -r 56162e446004 -r 893655fa55f9 test-data/reads.right.fq.gz
Binary file test-data/reads.right.fq.gz has changed