diff kallisto_quant.xml @ 1:7a9158bb6f98 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302

--- a/kallisto_quant.xml	Sat Aug 05 04:02:28 2017 -0400
+++ b/kallisto_quant.xml	Mon Aug 07 13:25:33 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.0">
+<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1">
     <description>- quantify abundances of RNA-Seq transcripts</description>
     <macros>
         <import>macros.xml</import>
@@ -24,25 +24,20 @@
             #end if
             #if str($single_paired.single_paired_selector) == 'single':
                 --single
-                #set $single_reads = "' '".join(str($single_paired.reads).split(','))
+                #set $single_reads = $single_paired.reads
                 --fragment-length $single_paired.fragment_length
                 --sd $single_paired.sd
                 '$single_reads'
             #else:
                 #if str($single_paired.collection.collection_selector) == 'datasets':
-                    #set $forward_reads = str($single_paired.collection.forward).split(',')
-                    #set $reverse_reads = str($single_paired.collection.reverse).split(',')
+                    #set $forward_reads = $single_paired.collection.forward
+                    #set $reverse_reads = $single_paired.collection.reverse
                 #else:
-                    #set $forward_reads = [str($read.forward) for $read in $single_paired.collection.reads]
-                    #set $reverse_reads = [str($read.reverse) for $read in $single_paired.collection.reads]
+                    #set $forward_reads = $single_paired.collection.reads.forward
+                    #set $reverse_reads = $single_paired.collection.reads.reverse
                 #end if
-                #set $tuplexed_reads = zip($forward_reads, $reverse_reads)
-                #set $multiplexed_reads = []
-                #for read_pair in $tuplexed_reads:
-                    ${multiplexed_reads.extend([read for read in read_pair])}
-                #end for
-                #set $reads = "' '".join($multiplexed_reads)
-                '$reads'
+                #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
+                $reads
             #end if
             #if $pseudobam:
                 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
@@ -74,7 +69,7 @@
                 <option value="paired">Paired</option>
             </param>
             <when value="single">
-                <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />
+                <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
                 <param name="fragment_length" 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>
@@ -85,11 +80,11 @@
                         <option value="collection">Pair or list of pairs</option>
                     </param>
                     <when value="datasets">
-                        <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />
-                        <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />
+                        <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" collection_type="list:paired" label="Collection of reads" />
+                        <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
                     </when>
                 </conditional>
             </when>
@@ -113,8 +108,8 @@
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
             <param name="single_paired_selector" value="paired" />
             <param name="collection_selector" value="datasets" />
-            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq,mm10_chrM-2.f.fq,mm10_chrM-3.f.fq,mm10_chrM-4.f.fq,mm10_chrM-5.f.fq" />
-            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq,mm10_chrM-2.r.fq,mm10_chrM-3.r.fq,mm10_chrM-4.r.fq,mm10_chrM-5.r.fq" />
+            <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" />
         </test>
         <test>
@@ -123,37 +118,9 @@
             <param name="single_paired_selector" value="paired" />
             <param name="collection_selector" value="collection" />
             <param name="reads">
-                <collection type="list:paired">
-                    <element name="p1">
-                        <collection type="paired">
-                            <element name="forward" value="mm10_chrM-1.f.fq" />
-                            <element name="reverse" value="mm10_chrM-1.r.fq" />
-                        </collection>
-                    </element>
-                    <element name="p2">
-                        <collection type="paired">
-                            <element name="forward" value="mm10_chrM-2.f.fq" />
-                            <element name="reverse" value="mm10_chrM-2.r.fq" />
-                        </collection>
-                    </element>
-                    <element name="p3">
-                        <collection type="paired">
-                            <element name="forward" value="mm10_chrM-3.f.fq" />
-                            <element name="reverse" value="mm10_chrM-3.r.fq" />
-                        </collection>
-                    </element>
-                    <element name="p4">
-                        <collection type="paired">
-                            <element name="forward" value="mm10_chrM-4.f.fq" />
-                            <element name="reverse" value="mm10_chrM-4.r.fq" />
-                        </collection>
-                    </element>
-                    <element name="p5">
-                        <collection type="paired">
-                            <element name="forward" value="mm10_chrM-5.f.fq" />
-                            <element name="reverse" value="mm10_chrM-5.r.fq" />
-                        </collection>
-                    </element>
+                <collection type="paired">
+                    <element name="forward" value="mm10_chrM-1.f.fq" />
+                    <element name="reverse" value="mm10_chrM-1.r.fq" />
                 </collection>
             </param>
             <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />
@@ -163,7 +130,7 @@
             <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,mm10_chrM-2.f.fq,mm10_chrM-3.f.fq,mm10_chrM-4.f.fq,mm10_chrM-5.f.fq" />
+            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
             <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
         </test>
         <test>
@@ -182,7 +149,7 @@
             <param name="single_paired_selector" value="paired" />
             <param name="collection_selector" value="datasets" />
             <param name="pseudobam" value="true" />
-            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq" />
+            <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" />
             <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
             <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />