Repository 'kallisto_quant'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant

Changeset 10:4f9c4e6566e5 (2023-06-05)
Previous changeset 9:2568a3b975cb (2023-05-31)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
modified:
kallisto_quant.xml
macros.xml
b
diff -r 2568a3b975cb -r 4f9c4e6566e5 kallisto_quant.xml
--- a/kallisto_quant.xml Wed May 31 20:09:49 2023 +0000
+++ b/kallisto_quant.xml Mon Jun 05 22:06:44 2023 +0000
b
b'@@ -32,12 +32,12 @@\n                 \'$single_reads\'\n             #else:\n                 $single_paired.lib_type\n-                #if str($single_paired.collection.collection_selector) == \'datasets\':\n-                    #set $forward_reads = $single_paired.collection.forward\n-                    #set $reverse_reads = $single_paired.collection.reverse\n+                #if str($single_paired.single_paired_selector) == \'paired_single\':\n+                    #set $forward_reads = $single_paired.forward\n+                    #set $reverse_reads = $single_paired.reverse\n                 #else:\n-                    #set $forward_reads = $single_paired.collection.reads.forward\n-                    #set $reverse_reads = $single_paired.collection.reads.reverse\n+                    #set $forward_reads = $single_paired.reads.forward\n+                    #set $reverse_reads = $single_paired.reads.reverse\n                 #end if\n                 #set $reads = "\'%s\' \'%s\'" % ($forward_reads, $reverse_reads)\n                 $reads\n@@ -59,32 +59,22 @@\n         <conditional name="single_paired">\n             <param name="single_paired_selector" type="select" label="Single-end or paired reads">\n                 <option value="single" selected="true">Single-end</option>\n-                <option value="paired">Paired</option>\n+                <option value="paired_single">Paired.end (individual files)</option>\n+                <option value="paired_collection">Paired-end (collections)</option>\n             </param>\n             <when value="single">\n                 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n                 <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />\n                 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />\n             </when>\n-            <when value="paired">\n-                <conditional name="collection">\n-                    <param name="collection_selector" type="select" label="Collection or individual datasets">\n-                        <option value="datasets" selected="true">Individual files</option>\n-                        <option value="collection">Pair or list of pairs</option>\n-                    </param>\n-                    <when value="datasets">\n-                        <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />\n-                        <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />\n-                    </when>\n-                    <when value="collection">\n-                        <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />\n-                    </when>\n-                </conditional>\n-                <param name="lib_type" type="select" label="Library strandness information">\n-                    <option value="">Unstranded</option>\n-                    <option value="--fr-stranded">Strand specific reads, first read forward</option>\n-                    <option value="--rf-stranded">Strand specific reads, first read reverse</option>\n-                </param>\n+            <when value="paired_single">\n+                <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />\n+                <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />\n+                <expand macro="macro_lib_type"/>\n+            </when>\n+            <when value="paired_collection">\n+                <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />\n+                <expand macro="macro_lib_type"/>\n             </when>\n         </conditional>\n         <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform se'..b'me_source" value="history" />\n             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="datasets" />\n+            <param name="single_paired_selector" value="paired_single" />\n             <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />\n             <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />\n             <param name="lib_type" value="--fr-stranded"/>\n@@ -146,8 +134,7 @@\n         <test>\n             <param name="reference_transcriptome_source" value="history" />\n             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="collection" />\n+            <param name="single_paired_selector" value="paired_collection" />\n             <param name="reads">\n                 <collection type="paired">\n                     <element name="forward" value="mm10_chrM-1.f.fq" />\n@@ -160,15 +147,13 @@\n             <param name="reference_transcriptome_source" value="history" />\n             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n             <param name="single_paired_selector" value="single" />\n-            <param name="collection_selector" value="collection" />\n             <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />\n             <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />\n         </test>\n         <test>\n             <param name="reference_transcriptome_source" value="history" />\n             <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="datasets" />\n+            <param name="single_paired_selector" value="paired_single" />\n             <param name="pseudobam" value="true" />\n             <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />\n             <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />\n@@ -177,8 +162,7 @@\n         </test>\n         <test>\n             <param name="reference_transcriptome_source" value="cached" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="datasets" />\n+            <param name="single_paired_selector" value="paired_single" />\n             <param name="pseudobam" value="true" />\n             <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />\n             <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />\n@@ -188,8 +172,7 @@\n         <test>\n             <param name="reference_transcriptome_source" value="history" />\n             <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="datasets" />\n+            <param name="single_paired_selector" value="paired_single" />\n             <param name="fusion" value="true" />\n             <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />\n             <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />\n@@ -198,8 +181,7 @@\n         <test>\n             <param name="reference_transcriptome_source" value="history" />\n             <param name="reference" ftype="fasta" value="transcripts.fasta" />\n-            <param name="single_paired_selector" value="paired" />\n-            <param name="collection_selector" value="datasets" />\n+            <param name="single_paired_selector" value="paired_single" />\n             <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />\n             <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />\n             <conditional name="genomebam_option">\n'
b
diff -r 2568a3b975cb -r 4f9c4e6566e5 macros.xml
--- a/macros.xml Wed May 31 20:09:49 2023 +0000
+++ b/macros.xml Mon Jun 05 22:06:44 2023 +0000
b
@@ -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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