diff star_fusion.xml @ 3:137942fac417 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"

--- a/star_fusion.xml	Fri Sep 07 11:30:25 2018 -0400
+++ b/star_fusion.xml	Mon Jan 06 11:08:46 2020 -0500
@@ -1,7 +1,6 @@
-<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01">
+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3+galaxy1" profile="17.01">
     <description>detect fusion genes in RNA-Seq data</description>
     <requirements>
-        <!-- Bio-conda -->
         <requirement type="package" version="0.5.4">star-fusion</requirement>
     </requirements>
 
@@ -26,68 +25,60 @@
     <version_command>STAR-Fusion --version  2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
 
     <command><![CDATA[
-        ## 1. ensure the blastn file is provided as *.gz
-        if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then
-            gzip_suffix='' ;
-        else
-            ## Older versions of gzip do not support the -k option to keep
-            ## the original file - this should be an universion solution
-            
-            gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' &&
-            gzip_suffix='.gz' ;
-        fi &&
-        
-        ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
-        ## - @todo once write a decent STAR and STAR Fusion data manager
-        prep_genome_lib.pl
-            --genome_fa '${fasta_type.ownFile}'
-            --gtf '${geneModel}'
-            --blast_pairs "${blast_pairs}\$gzip_suffix"
-            --CPU \${GALAXY_SLOTS:-1}
-            --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
-        &&
+## 1. ensure the blastn file is provided as *.gz
+gzip -1 -c -- '${blast_pairs}' > blast_pairs.gz &&
 
-        ## 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}' ${read1} &&
+## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
+## - @todo once write a decent STAR and STAR Fusion data manager
+prep_genome_lib.pl
+    --genome_fa '${fasta_type.ownFile}'
+    --gtf '${geneModel}'
+    --blast_pairs blast_pairs.gz
+    --CPU \${GALAXY_SLOTS:-1}
+    --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+&&
+
+## Link in fastq files so they have appropriate extensions
+#if str($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
+    #if $input_params.right_fq:
+        #if $input_params.right_fq.is_of_type("fastq.gz"):
+            #set read2 = 'input_2.fastq.gz'
+        #else:
+            #set read2 = 'input_2.fastq'
         #end if
-        
-        ## 3. Run STAR-Fusion
-        STAR-Fusion
-            #if str($input_params.input_source) == "use_chimeric":
-                --chimeric_junction '${input_params.chimeric_junction}'
-            #else:
-                --left_fq ${read1}
-                #if $input_params.right_fq:
-                    --right_fq ${read2}
-                #end if
-            #end if
+        ln -f -s '${input_params.right_fq}' ${read2} &&
+    #end if
+#end if
 
-            --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+## 3. Run STAR-Fusion
+STAR-Fusion
+    #if str($input_params.input_source) == "use_chimeric":
+        --chimeric_junction '${input_params.chimeric_junction}'
+    #else:
+        --left_fq ${read1}
+        #if $input_params.right_fq:
+            --right_fq ${read2}
+        #end if
+    #end if
 
-        #if str($params.settingsType) == "full":
-            --min_junction_reads $params.min_junction_reads
-            --min_sum_frags $params.min_sum_frags
-            --max_promiscuity $params.max_promiscuity
-            --min_novel_junction_support $params.min_novel_junction_support
-            --min_alt_pct_junction $params.min_alt_pct_junction
-            --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
-            --E $params.E
-        #end if
+    --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+
+#if str($params.settingsType) == "full":
+    --min_junction_reads $params.min_junction_reads
+    --min_sum_frags $params.min_sum_frags
+    --max_promiscuity $params.max_promiscuity
+    --min_novel_junction_support $params.min_novel_junction_support
+    --min_alt_pct_junction $params.min_alt_pct_junction
+    --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
+    --E $params.E
+#end if
     ]]></command>
 
     <inputs>