diff pbgcpp.xml @ 0:a6d93d0d5328 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp commit d8032f67869704a4f9308796d748966d1f4760ae

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pbgcpp.xml	Wed Mar 01 22:42:22 2023 +0000
@@ -0,0 +1,147 @@
+<tool id="pbgcpp" name="pbgcpp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Compute genomic consensus and call variants using PacBio reads mapped to a reference.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## set up files
+        #if $reference_source.reference_source_selector == 'history':
+            #set ref_fn = 'reference.fa'
+            ln -f -s '$reference_source.ref_file' '$ref_fn' &&
+        #else:
+            #set ref_fn = $reference_source.ref_file.fields.path
+        #end if
+
+        ln -s '$input' 'input.bam' &&
+        ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
+
+        ## set up the outputs
+        #set output_line = ','.join('output.' + str(x) for x in $output_selector)
+
+        ## run variantCaller
+        gcpp 
+        --num-threads \${GALAXY_SLOTS:-4}
+        --reference '$ref_fn'
+        --output $output_line
+        'input.bam'
+    ]]></command>
+    <inputs>
+        <!-- from tools-iuc minimap2 wrapper -->
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+                <option value="cached">Use a built-in genome index</option>
+                <option value="history">Use a genome from history and build index</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No reference genomes are available" />
+                    </options>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <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="input" format="bam" label="bam" help="The input BAM alignment file" />
+        <!-- Output Options -->
+        <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Output formats">
+            <!-- Use the format's extension as the value, so we can use it directly in the output_line constructor. -->
+            <option value="fa" selected="true">Computed consensus (fasta)</option>
+            <option value="vcf">Variants (vcf)</option>
+            <option value="gff">Variants (gff)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="fa" format="fasta" from_work_dir="output.fa" label="${tool.name} on ${on_string} (consensus)">
+            <filter>output_selector and 'fa' in output_selector</filter>
+        </data>
+        <data name="gff" format="gff" from_work_dir="output.gff" label="${tool.name} on ${on_string} (gff)">
+            <filter>output_selector and 'gff' in output_selector</filter>
+        </data>
+        <data name="vcf" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string} (vcf)">
+            <filter>output_selector and 'vcf' in output_selector</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- test1: basic test (output from pbmm2 1.10.0) -->
+        <test expect_num_outputs="1">
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="bnd-ref.fasta"/>
+            <param name="input" value="pbmm2_3.bam"/>
+            <param name="output_selector" value="fa"/>
+            <output name="fa" ftype="fasta" file="pbgcpp_test1_out.fa"/>
+        </test>
+        <!-- test2: output selector -->
+        <test  expect_num_outputs="3">
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="bnd-ref.fasta"/>
+            <param name="input" value="pbmm2.bam"/>
+            <param name="output_selector" value="fa,gff,vcf"/>
+            <output name="fa" ftype="fasta" file="pbgcpp_test2_out.fa"/>
+            <output name="gff" ftype="gff">
+                <assert_contents>
+                    <has_text text="gff-version 3" />
+                </assert_contents>
+            </output>
+            <output name="vcf" ftype="vcf">
+                <assert_contents>
+                    <has_text text="fileformat=VCFv4.2" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test3: cached genome -->
+        <test>
+            <param name="reference_source_selector" value="cached" />
+            <param name="ref_file" value="bnd-ref"/>
+            <param name="input" value="pbmm2_3.bam"/>
+            <param name="output_selector" value="fa"/>
+            <output name="fa" ftype="fasta" file="pbgcpp_test3_out.fa"/>
+        </test>
+    </tests>
+        <help><![CDATA[
+**What it does**
+
+Compute genomic consensus and call variants relative to the reference.
+
+This tool requires a PacBio BAM file.
+
+You can create one by mapping PacBio reads to the reference genome with
+the `pbmm2 <root?tool_id=pbmm2>`__ tool. When doing this, you have to
+input CLR reads to pbmm2 in [unaligned] BAM format, not fastq or fasta. This is
+because the pbgcpp algorithm uses additional information stored in the
+unaligned BAM format that PacBio uses.
+
+**NOTE**: The pbgcpp tool used to be called GenomicConsensus.  It works for PacBio Sequel data and RS data with the P6-C4 chemistry.
+
+--------------
+
+pbgcpp is Pacific Biosciences’ tool to generate accurate reference
+contigs. It takes an alignment in the form of a BAM file and polishes
+the references with the provided subreads from the alignment. It uses
+the Arrow algorithm in multi-molecule consensus setting and can reach up
+to QV60 at coverage 100. pbgcpp is the successor of the venerable
+GenomicConsensus suite which has reached EOL.
+
+See the `Pacific Biosciences GitHub
+page <https://github.com/PacificBiosciences/pbbioconda>`__ for more
+information.
+
+**Input**: Aligned subreads in PacBio BAM format (.bam). Compatible with PacBio Sequel data and RS data with the P6-C4 chemistry.
+
+**Output**: Polished contigs in .fasta format.
+
+**Why am I getting “Missing valid chemistry from input file, is this a
+proper PBBAM input file?”**
+
+pbgcpp expects metadata in the bamfile that most aligners (like
+minimap2) don’t include by default. Align the PacBio reads file using
+pbmm2.
+
+        ]]></help>
+    <expand macro="creator"/>
+</tool>