diff bowtie2_wrapper.xml @ 16:8ccbdbe9a695 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
author iuc
date Thu, 01 Jun 2017 11:14:22 -0400
parents 43d12513224b
children 66f992977578
line wrap: on
line diff
--- a/bowtie2_wrapper.xml	Thu Jun 01 06:47:03 2017 -0400
+++ b/bowtie2_wrapper.xml	Thu Jun 01 11:14:22 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="2.3.2.1" profile="17.01">
+<tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
@@ -22,6 +22,7 @@
         ## Link in the input files, so bowtie2 can tell their type
 
         #set compressed="False"
+        #set reads_are_fastq = True
         #if str($library.type) == 'paired':
             #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read1 = "input_f.fastq.gz"
@@ -29,6 +30,9 @@
             #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read1 = "input_f.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_1.is_of_type('fasta'):
+                #set reads_are_fastq = False
+                #set read1 = "input_f.fasta"
             #else:
                 #set read1 = "input_f.fastq"
             #end if
@@ -40,6 +44,8 @@
             #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read2 = "input_r.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_2.is_of_type('fasta'):
+                #set read2 = "input_r.fasta"
             #else:
                 #set read2 = "input_r.fastq"
             #end if
@@ -51,6 +57,9 @@
             #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read1 = "input_f.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_1.forward.is_of_type('fasta'):
+                #set reads_are_fastq = False
+                #set read1 = "input_f.fasta"
             #else:
                 #set read1 = "input_f.fastq"
             #end if
@@ -62,6 +71,8 @@
             #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read2 = "input_r.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_1.reverse.is_of_type("fasta"):
+                #set read2 = "input_r.fasta"
             #else:
                 #set read2 = "input_r.fastq"
             #end if
@@ -74,6 +85,9 @@
             #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read1 = "input_il.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_1.is_of_type("fasta"):
+                #set reads_are_fastq = False
+                #set read1 = "input_il.fasta"
             #else:
                 #set read1 = "input_il.fastq"
             #end if
@@ -85,6 +99,9 @@
             #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
                 #set read1 = "input_f.fastq.bz2"
                 #set compressed = "BZ2"
+            #else if $library.input_1.is_of_type("fasta"):
+                #set reads_are_fastq = False
+                #set read1 = "input_f.fasta"
             #else:
                 #set read1 = "input_f.fastq"
             #end if
@@ -101,7 +118,12 @@
         ## index file path
         -x '$index_path'
 
-        ## Fastq inputs
+        ## Input reads are fasta?
+        #if not reads_are_fastq:
+            -f
+        #end if
+
+        ## Input reads
         #if str( $library.type ) == "single":
             -U '${read1}'
             #if str( $library.unaligned_file ) == "true":
@@ -310,28 +332,28 @@
             </param>
 
             <when value="single">
-                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
+                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
 
                 <expand macro="align_unalign" />
 
             </when>
             <when value="paired">
-                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
-                <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
+                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
+                <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
 
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
 
             </when>
             <when value="paired_collection">
-                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
+                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
 
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
 
             </when>
             <when value="paired_interleaved">
-                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;. --interleaved"/>
+                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
                
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
@@ -728,6 +750,18 @@
             <param name="own_file" value="bowtie2-ref.fasta" />
             <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
         </test>
+        <test>
+            <!-- test fasta input -->
+            <param name="type" value="paired"/>
+            <param name="paired_options_selector" value="no"/>
+            <param name="unaligned_file" value="false"/>
+            <param name="analysis_type_selector" value="simple"/>
+            <param name="source" value="history" />
+            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
+            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
+            <param name="own_file" value="bowtie2-ref.fasta" />
+            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
+        </test>
     </tests>
 
     <help><![CDATA[