diff hisat2.xml @ 10:da8d655e2154 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890

--- a/hisat2.xml	Tue Apr 04 08:15:43 2017 -0400
+++ b/hisat2.xml	Mon Apr 10 17:40:42 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="2.0.5">
+<tool id="hisat2" name="HISAT2" version="2.0.5" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -20,6 +20,9 @@
             ln -s '${spliced_options.known_splice_gtf}' splice_sites.gtf &&
             hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
         #end if
+
+        @FASTQGZ_SETUP@
+
         #if $reference_genome.reference_genome_source == "history":
             ln -s '$reference_genome.history_item' genome.fa &&
             hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&
@@ -28,19 +31,28 @@
             #set index_path = $reference_genome.index.fields.path
         #end if
         hisat2 -p \${GALAXY_SLOTS:-1} -x '${index_path}'
-        #if str($input_format.paired.paired_selector) == 'paired':
-            -1 '${input_format.paired.reads_f}' -2 '${input_format.paired.reads_r}'
-            @paired_end_options@
-        #else if str($input_format.paired.paired_selector) == 'paired_collection':
-            -1 '${input_format.paired.reads.forward}' -2 '${input_format.paired.reads.reverse}'
+        #if str($input_format.paired.paired_selector) != 'single':
+            -1 '${read1}' -2 '${read2}'
             @paired_end_options@
         #else:
-            -U '${input_format.paired.reads}'
+            -U '${read1}'
             #if str( $input_format.paired.unaligned_file ) == "true":
-                --un '$output_unaligned_reads_l'
+                #if $compressed == "GZ":
+                    --un-gz '$output_unaligned_reads_l'
+                #else if $compressed == "BZ2":
+                    --un-gz '$output_unaligned_reads_l'
+                #else:
+                    --un '$output_unaligned_reads_l'
+                #end if
             #end if
             #if str( $input_format.paired.aligned_file ) == "true":
-                --al '$output_aligned_reads_l'
+                #if $compressed == "GZ":
+                    --al-gz '$output_aligned_reads_l'
+                #else if $compressed == "BZ2":
+                    --al-bz2 '$output_aligned_reads_l'
+                #else:
+                    --al '$output_aligned_reads_l'
+                #end if
             #end if
         #end if
         #if $input_format.input_format_selector == 'fasta':
@@ -125,7 +137,7 @@
                 <expand macro="paired_input_conditional" ftype="fasta" />
             </when>
             <when value="fastq">
-                <expand macro="paired_input_conditional" ftype="fastq" />
+                <expand macro="paired_input_conditional" ftype="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
             </when>
         </conditional>
         <conditional name="reference_genome">
@@ -427,6 +439,36 @@
             <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
             <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
         </test>
+        <test><!-- Ensure fastqsanger.gz works -->
+            <param name="input_format_selector" value="fastq" />
+            <param name="paired_selector" value="paired" />
+            <param name="reference_genome_source" value="history" />
+            <param name="history_item" value="phiX.fa" ftype="fasta" />
+            <param name="input_options_selector" value="advanced" />
+            <param name="trim_three" value="15" />
+            <param name="trim_five" value="15" />
+            <param name="reads_f" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />
+            <param name="reads_r" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />
+            <param name="paired_end_options_selector" value="advanced" />
+            <param name="no_mixed" value="True" />
+            <param name="no_discordant" value="True" />
+            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
+        </test>
+        <test><!-- Ensure fastqsanger.bz2 works -->
+            <param name="input_format_selector" value="fastq" />
+            <param name="paired_selector" value="paired" />
+            <param name="reference_genome_source" value="history" />
+            <param name="history_item" value="phiX.fa" ftype="fasta" />
+            <param name="input_options_selector" value="advanced" />
+            <param name="trim_three" value="15" />
+            <param name="trim_five" value="15" />
+            <param name="reads_f" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />
+            <param name="reads_r" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />
+            <param name="paired_end_options_selector" value="advanced" />
+            <param name="no_mixed" value="True" />
+            <param name="no_discordant" value="True" />
+            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
+        </test>
     </tests>
     <help>
         <![CDATA[