diff arriba.xml @ 4:77021ad5037d draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"

--- a/arriba.xml	Fri Oct 08 20:44:25 2021 +0000
+++ b/arriba.xml	Sat Oct 09 15:41:49 2021 +0000
@@ -20,7 +20,7 @@
     #end if
     ln -f -s '${input_params.right_fq}' ${read2} &&
     #if str($input_params.index.index_source) == "history"
-        #set $star_index_dir = $input_params.index.star_index.files_path
+        #set $star_index_dir = $input_params.index.star_index.extra_files_path
     #end if
     STAR 
     --runThreadN \${GALAXY_SLOTS:-1} 
@@ -56,29 +56,31 @@
 #end if
     -a '$genome_assembly'
     -g '$gtf'
-    #if '$blacklist'
+    #if $blacklist
         -b '$blacklist'
+    #else
+        -f 'blacklist'
     #end if
-    #if '$protein_domains'
+    #if $protein_domains
         -p '$protein_domains'
     #end if
-    #if '$known_fusions'
+    #if $known_fusions
         -k '$known_fusions'
     #end if
-    #if '$tags'
+    #if $tags
         -t '$tags'
     #end if
     -o fusions.tsv
     -O fusions.discarded.tsv 
 #if str($input_params.input_source) == "use_fastq"
-    && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
+    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
     && samtools index Aligned.sortedByCoord.out.bam
 #elif str($visualization.do_viz) == "yes"
-    && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
+    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
     && samtools index Aligned.sortedByCoord.out.bam
 #end if
 #if str($visualization.do_viz) == "yes"
-draw_fusions.R \
+&& draw_fusions.R 
     --fusions=fusions.tsv 
     --alignments=Aligned.sortedByCoord.out.bam 
     --output=fusions.pdf 
@@ -87,7 +89,7 @@
     --cytobands='$visualization.cytobands'
     #end if
     #if '$protein_domains'
-    --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3
+    --proteinDomains='$protein_domains'
     #end if
 #end if
 
@@ -129,11 +131,12 @@
         <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
         <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
         <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/>
-        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/>
+        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
         <param name="known_fusions" argument="-k" type="data" format="tabular"  optional="true" label="File containing known fusions">
             <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
         </param>
-        <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/>
+        <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
+               help="This can be the known fusions if that input has a third column with a name"/>
         <conditional name="visualization">
             <param name="do_viz" type="select" label="Generate visualization">
                 <option value="yes">Yes</option>
@@ -152,10 +155,29 @@
         <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
             <filter>input_params['input_source'] == "use_fastq"</filter>
         </data> 
-        <data name="fusions_png" format="png" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
+        <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
             <filter>visualization['do_viz'] == "yes"</filter>
         </data> 
     </outputs>
+    <tests>
+        <!-- Test 1 - From exisitng BAM -->
+        <test> 
+            <conditional name="input_params">
+                <param name="input_source" value="use_star"/>
+                <param name="input" ftype="sam" value="Aligned.out.sam"/>
+            </conditional>
+            <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
+            <param name="gtf" ftype="gtf" value="genome.gtf"/>
+            <conditional name="visualization">
+                <param name="do_viz" value="no"/>
+            </conditional>
+            <output name="fusions">
+                <assert_contents>
+                    <has_text_matching expression="BCR\tABL1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
 ** Arriba **