# HG changeset patch
# User iuc
# Date 1686002732 0
# Node ID 81c9f0ba13d2416475fd4aa8927802801b25d4ff
# Parent  8bb5d2582782672ad7d500d954f713f0c249245c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f

diff -r 8bb5d2582782 -r 81c9f0ba13d2 kallisto_quant.xml
--- a/kallisto_quant.xml	Wed May 31 20:08:38 2023 +0000
+++ b/kallisto_quant.xml	Mon Jun 05 22:05:32 2023 +0000
@@ -32,12 +32,12 @@
                 '$single_reads'
             #else:
                 $single_paired.lib_type
-                #if str($single_paired.collection.collection_selector) == 'datasets':
-                    #set $forward_reads = $single_paired.collection.forward
-                    #set $reverse_reads = $single_paired.collection.reverse
+                #if str($single_paired.single_paired_selector) == 'paired_single':
+                    #set $forward_reads = $single_paired.forward
+                    #set $reverse_reads = $single_paired.reverse
                 #else:
-                    #set $forward_reads = $single_paired.collection.reads.forward
-                    #set $reverse_reads = $single_paired.collection.reads.reverse
+                    #set $forward_reads = $single_paired.reads.forward
+                    #set $reverse_reads = $single_paired.reads.reverse
                 #end if
                 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
                 $reads
@@ -59,32 +59,22 @@
         <conditional name="single_paired">
             <param name="single_paired_selector" type="select" label="Single-end or paired reads">
                 <option value="single" selected="true">Single-end</option>
-                <option value="paired">Paired</option>
+                <option value="paired_single">Paired.end (individual files)</option>
+                <option value="paired_collection">Paired-end (collections)</option>
             </param>
             <when value="single">
                 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
                 <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
                 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
             </when>
-            <when value="paired">
-                <conditional name="collection">
-                    <param name="collection_selector" type="select" label="Collection or individual datasets">
-                        <option value="datasets" selected="true">Individual files</option>
-                        <option value="collection">Pair or list of pairs</option>
-                    </param>
-                    <when value="datasets">
-                        <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
-                        <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
-                    </when>
-                    <when value="collection">
-                        <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
-                    </when>
-                </conditional>
-                <param name="lib_type" type="select" label="Library strandness information">
-                    <option value="">Unstranded</option>
-                    <option value="--fr-stranded">Strand specific reads, first read forward</option>
-                    <option value="--rf-stranded">Strand specific reads, first read reverse</option>
-                </param>
+            <when value="paired_single">
+                <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
+                <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
+                <expand macro="macro_lib_type"/>
+            </when>
+            <when value="paired_collection">
+                <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
+                <expand macro="macro_lib_type"/>
             </when>
         </conditional>
         <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" help="It allows to learn 
@@ -123,8 +113,7 @@
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
             <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
             <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
@@ -132,8 +121,7 @@
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
             <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
             <param name="lib_type" value="--fr-stranded"/>
@@ -146,8 +134,7 @@
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="collection" />
+            <param name="single_paired_selector" value="paired_collection" />
             <param name="reads">
                 <collection type="paired">
                     <element name="forward" value="mm10_chrM-1.f.fq" />
@@ -160,15 +147,13 @@
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
             <param name="single_paired_selector" value="single" />
-            <param name="collection_selector" value="collection" />
             <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
             <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
         </test>
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="pseudobam" value="true" />
             <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
             <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
@@ -177,8 +162,7 @@
         </test>
         <test>
             <param name="reference_transcriptome_source" value="cached" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="pseudobam" value="true" />
             <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
             <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
@@ -188,8 +172,7 @@
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="fusion" value="true" />
             <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
             <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
@@ -198,8 +181,7 @@
         <test>
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="transcripts.fasta" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
+            <param name="single_paired_selector" value="paired_single" />
             <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />
             <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />
             <conditional name="genomebam_option">
diff -r 8bb5d2582782 -r 81c9f0ba13d2 macros.xml
--- a/macros.xml	Wed May 31 20:08:38 2023 +0000
+++ b/macros.xml	Mon Jun 05 22:05:32 2023 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">0.48.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement>
@@ -32,4 +32,11 @@
             </when>
         </conditional>
     </xml>
+    <xml name="macro_lib_type">
+        <param name="lib_type" type="select" label="Library strandness information">
+            <option value="">Unstranded</option>
+            <option value="--fr-stranded">Strand specific reads, first read forward</option>
+            <option value="--rf-stranded">Strand specific reads, first read reverse</option>
+        </param>
+    </xml>
 </macros>
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