diff pacu_snp.xml @ 0:7ba3e44093c9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu commit 4290547cefb0459595f28fbba063f2cf58b35086

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pacu_snp.xml	Tue Aug 13 13:45:25 2024 +0000
@@ -0,0 +1,137 @@
+<tool id="pacu_snp" name="PACU" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        PACU_galaxy
+
+        ## Input files
+        --ref-fasta '$input.ref_fasta'
+        --ref-fasta-name '$input.ref_fasta.element_identifier'
+
+        #for $bam in $input.bam_ilmn:
+            #if $bam:
+                --bam-ilmn $bam '$bam.element_identifier'
+            #end if
+        #end for
+
+        #for $bam in $input.bam_ont:
+            #if $bam:
+                --bam-ont $bam '$bam.element_identifier'
+            #end if
+        #end for
+
+        ## Excluded regions
+        #if $input.ref_bed:
+            --ref-bed $input.ref_bed
+        #end if
+
+        ## Tree building method
+        #if $params.tree_method == 'mega':
+            --use-mega
+        #end if
+
+        ## Other parameters
+        --min-global-depth $params.min_global_depth
+        $params.skip_gubbins
+
+        ## Output files
+        --output-html '$html'
+        --output '$html.files_path'
+
+        ## Variant filters
+        --min-snp-af $filtering.min_snp_af
+        --min-snp-qual $filtering.min_snp_qual
+        --min-snp-depth $filtering.min_snp_depth
+        --min-snp-dist $filtering.min_snp_dist
+
+        ## Other options
+        --threads \${GALAXY_SLOTS}
+        ]]>
+    </command>
+    <inputs>
+        <!-- Input files -->
+        <section name="input" title="Input files" expanded="true">
+            <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
+            <param argument="--bam-ilmn" type="data" format="bam" multiple="true" optional="true"
+                   label="BAM files (Illumina)"
+                   help="Make sure the reads are mapped to the reference selected above."/>
+            <param argument="--bam-ont" type="data" format="bam" multiple="true" optional="true" label="BAM files (ONT)"
+                   help="Make sure the reads are mapped to the reference selected above."/>
+            <param argument="--ref-bed" type="data" format="bed" optional="true" label="Excluded regions BED file" help="BED file with (pro)phage or other regions in the reference genome to be omitted from the SNP analysis."/>
+        </section>
+
+        <!-- Parameters -->
+        <section name="params" title="Parameters" expanded="False">
+            <param name="tree_method" type="select" label="Tree building method"
+                   help="MEGA is not part of the Conda installation and may be unavailable.">
+                <option value="iqtree" selected="true">IQ-TREE</option>
+                <option value="mega">MEGA X</option>
+            </param>
+            <param argument="--skip-gubbins" type="boolean" label="Skip Gubbins" checked="false"
+                   truevalue="--skip-gubbins" falsevalue=""
+                   help="Skips recombination detection using Gubbins, this option can be used to work with fragmented reference genomes."/>
+            <param argument="--min-global-depth" type="integer" label="Min. global depth" value="5" min="0" max="100"
+                   help="Minimum depth across all samples for a position to be included in the SNP analysis."/>
+        </section>
+
+        <!-- Variant filtering -->
+        <section name="filtering" title="Variant filters" expanded="false">
+            <param argument="--min-snp-af" type="float" value="0.66" min="0.0" max="1.0" label="Min. allele frequency"/>
+            <param argument="--min-snp-depth" type="integer" value="5" min="0" label="Min. depth"/>
+            <param argument="--min-snp-qual" type="integer" value="50" min="0" max="255" label="Min. SNP quality"/>
+            <param argument="--min-snp-dist" type="integer" value="10" min="0" max="100"
+                   label="Min. distance between SNPs"/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="html" format="html" label="PACU (${input.ref_fasta.element_identifier})"/>
+    </outputs>
+    <tests>
+        <test>
+            <section name="input">
+                <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+                <param name="bam_ilmn" value="TIAC1151.bam,TIAC1153.bam,TIAC1660.bam"/>
+                <param name="bam_ont" value="TIAC1638-R9-ds.bam,TIAC1151-R10-ds.bam"/>
+            </section>
+            <section name="params">
+                <param name="tree_method" value="iqtree"/>
+            </section>
+            <output name="html" ftype="html">
+                <assert_contents>
+                    <has_text text="PACU report"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <section name="input">
+                <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+                <param name="ref_bed" value="NC_002695.2-sample.bed"/>
+                <param name="bam_ilmn" value="TIAC1151.bam,TIAC1153.bam,TIAC1660.bam"/>
+                <param name="bam_ont" value="TIAC1638-R9-ds.bam,TIAC1151-R10-ds.bam"/>
+            </section>
+            <section name="params">
+                <param name="tree_method" value="iqtree"/>
+            </section>
+            <output name="html" ftype="html">
+                <assert_contents>
+                    <has_text text="PACU report"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        **Warning:** At least four input BAM files are required for bootstrapping (these can be a mix of Illumina / ONT
+        datasets).
+
+        **Note:** You can use the *'PACU - mapping'* tool in Galaxy to map Illumina or ONT reads to the reference
+        genome.
+    </help>
+    <expand macro="citations"/>
+</tool>