# HG changeset patch
# User iuc
# Date 1620809683 0
# Node ID 5b60313a6ce72d75c12fb5930425ae1b970a10d6
# Parent  26d5493b20b68de8d4899201e635a4d176ea1865
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"

diff -r 26d5493b20b6 -r 5b60313a6ce7 trinity.xml
--- a/trinity.xml	Fri Mar 19 21:43:30 2021 +0000
+++ b/trinity.xml	Wed May 12 08:54:43 2021 +0000
@@ -20,12 +20,39 @@
             ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
             ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
         #end if
+        #if $pool.pool_mode == "Yes":
+            #if str($pool.inputs.paired_or_single) == "single":
+                #for i, f in enumerate($pool.inputs.input):
+                    ln -s '$f' input${i}.${f.ext} &&
+                #end for
+            #elif str($pool.inputs.paired_or_single) == "paired":
+                #for i, f in enumerate($pool.inputs.left_input):
+                    ln -s '$f' left_input${i}.${f.ext} &&
+                #end for
+                #for i, f in enumerate($pool.inputs.right_input):
+                    ln -s '$f' right_input${i}.${f.ext} &&
+                #end for
+            #elif str($pool.inputs.paired_or_single) == "paired_collection":
+                #for i, f in enumerate($pool.inputs.pair_input):
+                    ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' &&
+                    ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' &&
+                #end for
+            #end if
+        #elif $pool.pool_mode == "No":
+            #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
+                ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' &&
+                ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' &&
+            #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
+                ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' &&
+            #end if
+        #end if
+
         Trinity --no_version_check
 
         ## Inputs
         #if $pool.pool_mode == "Yes":
             #if str($pool.inputs.paired_or_single) == "single":
-                --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) }
+                --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) }
                 #if $pool.inputs.input[0].is_of_type('fasta'):
                     --seqType fa
                 #else:
@@ -36,9 +63,9 @@
                     --SS_lib_type $pool.inputs.strand.library_type
                 #end if
             #elif str($pool.inputs.paired_or_single) == "paired":
-                --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) }
+                --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) }
 
-                --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) }
+                --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) }
 
                 #if $pool.inputs.left_input[0].is_of_type('fasta'):
                     --seqType fa
@@ -47,8 +74,8 @@
                 #end if
                 @COMMAND_PAIRED_STRAND_JACCARD@
             #elif str($pool.inputs.paired_or_single) == "paired_collection":
-                --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) }
-                --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) }
+                --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
+                --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
                 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
                     --seqType fa
                 #else:
@@ -58,9 +85,9 @@
             #end if
         #elif $pool.pool_mode == "No":
             #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
-                --left $pool.inputs.pair_input.forward
+                --left 'left_input.${$pool.inputs.pair_input.forward.ext}'
 
-                --right $pool.inputs.pair_input.reverse
+                --right 'right_input.${pool.inputs.pair_input.reverse.ext}'
 
                 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
                     --seqType fa
@@ -69,9 +96,9 @@
                 #end if
                 @COMMAND_PAIRED_STRAND_JACCARD@
             #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
-                --single $pool.inputs.input
+                --single 'input.${pool.inputs.input.ext}'
 
-                #if  $pool.inputs.input.is_of_type('fasta'):
+                #if $pool.inputs.input.is_of_type('fasta'):
                     --seqType fa
                 #else:
                     --seqType fq
@@ -239,8 +266,8 @@
             <param name="paired_or_single" value="unmerged_paired_collection"/>
             <param name="pair_input">
                 <collection type="paired">
-                    <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" />
-                    <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/>
+                    <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" />
+                    <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" />
                 </collection>
             </param>
             <param name="is_strand_specific" value="true"/>