diff star_fusion.xml @ 1:0b44456754e2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2

--- a/star_fusion.xml	Tue Sep 06 04:55:21 2016 -0400
+++ b/star_fusion.xml	Thu Apr 20 08:12:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01">
     <description>detect fusion genes in RNA-Seq data</description>
     <requirements>
         <!-- Bio-conda -->
@@ -46,15 +46,34 @@
             --CPU \${GALAXY_SLOTS:-1}
             --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
         &&
+
+        ## Link in fastq files so they have appropriate extensions
+        #if str($input_params.input_source) != "use_chimeric":
+            #if $input_params.left_fq.is_of_type("fastq.gz"):
+                #set read1 = 'input_1.fastq.gz'
+            #else:
+                #set read1 = 'input_1.fastq'
+            #end if
+            ln -f -s '${input_params.left_fq}' ${read1} &&
+
+            #if $input_params.right_fq:
+                #if $input_params.right_fq.is_of_type("fastq.gz"):
+                    #set read2 = 'input_2.fastq.gz'
+                #else:
+                    #set read2 = 'input_2.fastq'
+                #end if
+                ln -f -s '${input_params.right_fq}' ${read2} &&
+            #end if
+        #end if
         
         ## 3. Run STAR-Fusion
         STAR-Fusion
             #if str($input_params.input_source) == "use_chimeric":
                 --chimeric_junction '${input_params.chimeric_junction}'
             #else:
-                --left_fq '${input_params.left_fq}'
+                --left_fq ${read1}
                 #if $input_params.right_fq:
-                    --right_fq '${input_params.right_fq}'
+                    --right_fq ${read2}
                 #end if
             #end if
 
@@ -89,12 +108,12 @@
             <when value="use_fastq">
                 <param name="left_fq"
                        type="data"
-                       format="fastqsanger"
+                       format="fastqsanger,fastqsanger.gz"
                        argument="--left_fq"
                        label="left.fq file"/>
                 <param name="right_fq"
                        type="data"
-                       format="fastqsanger"
+                       format="fastqsanger,fastqsanger.gz"
                        optional="true"
                        argument="--right_fq"
                        label="right.fq file (actually optional, but highly recommended)"/>
@@ -121,7 +140,6 @@
                 <param name="ownFile"
                        type="data"
                        format="fasta"
-                       metadata_name="dbkey"
                        label="Select the reference genome (FASTA file)"/>
             </when>
         </conditional>
@@ -220,6 +238,23 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_source" value="use_fastq" />
+            <param name="left_fq" ftype="fastqsanger.gz" value="test1.fastqsanger.gz"/>
+            <param name="fasta_type_selector" value="history" />
+            <param name="ownFile" ftype="fasta" value="test1.fa" />
+            <param name="geneModel" ftype="gtf" value="test1.gtf" />
+            <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
+            <param name="settingsType" value="default" />
+            
+            <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
+            <output name="output_final">
+                <assert_contents>
+                    <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
+                    <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 **What it does**