diff arriba.xml @ 2:7420753b0671 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"

--- a/arriba.xml	Fri Oct 08 11:16:21 2021 +0000
+++ b/arriba.xml	Fri Oct 08 19:23:48 2021 +0000
@@ -19,9 +19,12 @@
         #set read2 = 'input_2.fastq'
     #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
+    #end if
     STAR 
     --runThreadN \${GALAXY_SLOTS:-1} 
-    --genomeDir /path/to/STAR_index 
+    --genomeDir $star_index_dir
     --genomeLoad NoSharedMemory 
     --readFilesIn $read1 $read2
     --readFilesCommand zcat 
@@ -70,9 +73,7 @@
     ]]></command>
     <inputs>
         <conditional name="input_params">
-            <param name="input_source"
-                   type="select"
-                   label="Use output from earlier STAR run or let Arriba running STAR">
+            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
                 <option value="use_star">Use output from earlier STAR</option>
                 <option value="use_fastq">Let Arriba control running STAR</option>
             </param>
@@ -93,6 +94,15 @@
                        format="fastqsanger,fastqsanger.gz"
                        argument="--right_fq"
                        label="right.fq file"/>
+                <conditional name="index">
+                    <param name="index_source" type="select" label="Arriba STAR index source">
+                        <option value="history">Arriba STAR index from your history</option>
+                    </param>
+                    <when value="history">
+                        <param name="star_index" argument="--genomeDir" type="data" format="txt" label="Arriba STAR index"
+                            help="generated by:  Arriba Reference"/>
+                    </when> 
+                </conditional>
             </when>
         </conditional>
         <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
@@ -219,6 +229,7 @@
       * Name=PROTEIN_DOMAIN_NAME;
       * gene_id=GENE_ID;
       * gene_name=GENE_NAME
+
     The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.
 
   - Structural variant calls from WGS