diff pbmm2.xml @ 2:55b7b257e12f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 commit ea74a1d7e62c0c7f878cf0d83f3539dfbb146b64

--- a/pbmm2.xml	Mon Mar 13 11:34:01 2023 +0000
+++ b/pbmm2.xml	Wed Feb 21 10:27:49 2024 +0000
@@ -20,6 +20,13 @@
         ## run pbmm2
         pbmm2 align 
         -j \${GALAXY_SLOTS:-4}
+        #if str($output_options.l):
+            -l $output_options.l
+        #end if
+        #if str($output_options.N):
+            -N $output_options.N
+        #end if
+        --preset $preset
         '$reads_fn' 
         '$ref_fn'
         out.aligned.bam
@@ -45,10 +52,21 @@
                 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
             </when>
         </conditional>
-        <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format." />
+        <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format"/>
+        <param argument="--preset" type="select"
+                label="Set alignment mode">
+                <option value="CCS">PacBio CCS or HiFi reads</option>
+                <option value="SUBREAD">PacBio CLR or raw subreads</option>
+                <option value="ISOSEQ">PacBio IsoSeq transcripts</option>
+                <option value="UNROLLED">Align entire raw ZMW</option>
+        </param>
+        <section name="output_options" title="Output Options" help="Sets -l, -N, --strip,  --split-by-sample,  --unmapped, --short-sa-cigar" expanded="False">
+            <param argument="-l" type="integer" min="0" label="Minimum mapped read length in basepairs" value="50" optional="true"/>
+            <param argument="-N" type="integer" min="0" label="Output at maximum N alignments for each read, 0 means no maximum" value="0" optional="true"/>
+        </section>
     </inputs>
     <outputs>
-        <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)" />
+        <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)"/>
     </outputs>
     <tests>
         <!-- test1: basic test -->
@@ -67,9 +85,10 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/>
             <param name="reads" value="out.aligned_subreads.bam"/>
+            <param name="preset" value="SUBREAD"/>
             <output name="bam">
                 <assert_contents>
-                    <has_size value="539464" delta="50000" />
+                    <has_size value="538329" delta="50000" />
                 </assert_contents>
             </output>
         </test>
@@ -108,5 +127,16 @@
 pbgcpp (previously known as GenomicConsensus).
 
         ]]></help>
+        <citations>
+            <citation type="bibtex">
+@misc{githubpbmm2,
+  author = {PacBio},
+  year = {2023},
+  title = {pbmm2},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/PacificBiosciences/pbmm2},
+}</citation>
+    </citations>
     <expand macro="creator"/>
 </tool>