diff ParSNP.xml @ 0:932410434dd1 draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ParSNP.xml	Fri Jan 24 17:45:42 2020 -0500
@@ -0,0 +1,198 @@
+<tool id="parsnp" name="ParSNP" version="1.2" profile="16.04">
+    <description>Efficient microbial core genome alignment and SNP detection</description>
+    <edam_topics>
+        <edam_topic>topic_3293</edam_topic>
+        <edam_topic>topic_0194</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2451</edam_operation>
+        <edam_operation>operation_0323</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="1.2">parsnp</requirement>
+    </requirements>
+    <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
+    export GENOME_DIR=\$(mktemp -d -p `pwd`)
+    #for $genome in $genomes
+        && ln -sf '$genome'
+        #if $adv.use_ids
+            \$GENOME_DIR/'$genome.element_identifier'
+        #else
+            \$GENOME_DIR/\$(basename '$genome')
+        #end if
+    #end for
+    && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${GALAXY_MEMORY_MB:-15000000} -d "\$GENOME_DIR"
+    #if $ref_or_gbk.ref_type == "fasta"
+        #if $ref_or_gbk.ref_genome.random_ref
+            -r '!'
+        #else
+            -r '$ref_or_gbk.ref_genome.reference'
+        #end if
+    #else
+        -g '
+        #for $gbk_file in $ref_or_gbk.genbank_files
+            #if $gbk_file
+                $gbk_file,
+            #end if
+        #end for
+        '
+    #end if
+    $adv.MUMi_or_curated.curated $adv.extend_lcb $adv.output_unaligned
+    #if $adv.query_genome
+        -q '$adv.query_genome'
+    #end if
+    #unless $adv.MUMi_or_curated.curated
+        $adv.MUMi_or_curated.MUMi.MUMi_only
+        #unless $adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution_default
+            -U '$adv.MUMi_or_curated.MUMi.max_mumi_distribution.max_distribution'
+        #end unless
+        #unless $adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance_default
+            -i '$adv.MUMi_or_curated.MUMi.max_mumi_distance.max_distance'
+        #end unless
+    #end unless
+    #unless $adv.min_anchor_len.anchor_default
+        -a '$adv.min_anchor_len.anchor'
+    #end unless
+    -C '$adv.d_value'
+    -z '$adv.lcb_size'
+    #if $adv.max_diag_diff.diag_diff_unit
+        -D '$adv.max_diag_diff.diag_diff_bp$adv.max_diag_diff.diag_diff_unit'
+    #else
+        -D '$adv.max_diag_diff.diag_diff'
+    #end if
+    #unless $adv.aligner == "muscle"
+        -n '$adv.aligner'
+    #end unless
+
+    ]]></command>
+    <inputs>
+        <!-- Inputs -->
+        <param name="genomes" type="data" multiple="true" argument="-d" format="fasta" label="Genomes/Contigs/Scaffolds" />
+        <conditional name="ref_or_gbk">
+            <param name="ref_type" type="select" label="Reference type">
+                <option value="fasta">Single fasta</option>
+                <option value="gbk">Multiple genbank files</option>
+            </param>
+            <when value="fasta">
+                <conditional name="ref_genome" label="Reference genome">
+                    <param name="random_ref" type="boolean" checked="false" label="Use random genome from above" />
+                    <when value="false">
+                        <param name="reference" type="data" format="fasta" label="Reference"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="gbk">
+                <param name="genbank_files" type="data" format="genbank" argument="-g" multiple="true" label="Reference genbank files" />
+            </when>
+        </conditional>
+        
+        <section name="adv" title="Advanced options" expanded="false">
+            <param name="query_genome" type="data" format="fasta" optional="true" label="Specify additional (assembled) query genome to use" />
+            <param name="use_ids" type="boolean" checked="true" label="Use dataset name or collection id's instead of file name in output" help="IDs must be valid POSIX file names" />
+            
+            <!-- Recombination filtration -->
+            <param name="filter_snp" type="boolean" checked="false"  truevalue="-x" falsevalue="" label="Enable filtering of SNPs located in PhiPack identified regions of recombination" />
+
+            <!-- MUM -->
+            <conditional name="min_anchor_len">
+                <param name="anchor_default" type="boolean" checked="true" label="Minimum ANCHOR length default" />
+                <when value="false">
+                    <param name="anchor" type="float" min="0" value="1.1" label="Minimum ANCHOR length"/>
+                </when>
+            </conditional>
+            <param name="d_value" type="integer" min="0" value="100" argument="-C" label="Maximal cluster D value"/>
+            <param name="lcb_size" type="integer" min="0" value="25" argument="-z" label="Min LCB size" />
+
+            <!-- MUMi -->
+            <conditional name="MUMi_or_curated">
+                <param name="curated" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Curated genome directory, use all genomes and ignore MUMi" />
+                <when value="">
+                    <conditional name="MUMi">
+                        <param name="MUMi_only" type="boolean" checked="false" truevalue="-M" falsevalue="" argument="-M" label="Only calculate MUMi and exit" />
+                        <when value="">
+                            <conditional name="max_mumi_distribution" label="Max MUMi distance value for MUMi distribution">
+                                <param name="max_distribution_default" type="boolean" checked="true" label="Default" />
+                                <when value="false">
+                                    <param name="max_distribution" type="float" value="1" />
+                                </when>
+                            </conditional>
+                            <conditional name="max_mumi_distance" label="Max MUMi distance">
+                                <param name="max_distance_default" type="boolean" checked="true" label="Autocutoff based on distribution of MUMi values" />
+                                <when value="false">
+                                    <param name="max_distance" type="float" value="1" />
+                                </when>
+                            </conditional>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+            
+            <!--LCB -->
+            <conditional name="max_diag_diff" label="Maximal diagonal difference">
+                <param name="diag_diff_unit" type="select" label="Unit">
+                    <option value="" selected="true">%</option>
+                    <option value="bp">Base pairs</option>
+                </param>
+                <when value="">
+                    <param name="diag_diff" type="float" min="0" max="1" value="0.12" />
+                </when>
+                <when value="bp">
+                    <param name="diag_diff_bp" type="integer" min="0" value="100" />
+                </when>
+            </conditional>
+            <param name="extend_lcb" type="boolean" checked="false" truevalue="-e" falsevalue="" argument="-e" label="Greedily extend LCBs" />              
+            <param name="aligner" type="select" argument="-n" label="Alignment program">
+                <option value="muscle" selected="true">muscle</option>
+                <option value="mafft">mafft</option>
+                <option value="fsa">fsa</option>
+                <option value="prank">prank</option>
+            </param>
+            <param name="output_unaligned" type="boolean" checked="false" truevalue="-u" falsevalue="" argument="-u" label="Output unaligned regions" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="tree" format="newick" from_work_dir="parsnp.tree" label="${tool.name} on ${on_string}: Newick formatted core genome SNP tree" />
+        <data name="vcf" format="vcf" from_work_dir="parsnp.vcf" label="${tool.name} on ${on_string}: SNPs used to infer phylogeny" />
+        <data name="ggr" format="ggr" from_work_dir="parsnp.ggr" label="${tool.name} on ${on_string}: Gingr formatted binary archive" />
+        <data name="xfma" format="xfma" from_work_dir="parsnp.xmfa" label="${tool.name} on ${on_string}: XMFA formatted multiple alignment" />
+        <data name="unaligned" format="txt" from_work_dir="parsnp.unaligned" label="${tool.name} on ${on_string}: Unaligned regions" >
+            <filter>adv['output_unaligned']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <param name="genomes" >
+                <collection type="list">
+                    <element name="test1" value="test-data/15596_genome.fasta" ftype="fasta" />
+                    <element name="test2" value="test-data/15602_genome.fasta" ftype="fasta" />
+                    <element name="test3" value="test-data/15599_genome.fasta" ftype="fasta" />
+                </collection>
+            </param>
+            <conditional name="ref_or_gbk">
+                <param name="ref_type" value="fasta" />
+                <conditional name="ref_genome">
+                    <param name="random_ref" value="false" />
+                    <param name="reference" value="test-data/15600_genome.fasta" ftype="fasta" />
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <conditional name="MUMi_or_curated">
+                    <param name="curated" value="-c" />
+                </conditional>
+            </section>
+            <output name="tree" checksum="sha256:66a2cc47666452fae008b546ab2bd5f9a06c7c7daca88e34e2be7a5cdd371137" ftype="newick" />
+            <output name="vcf" checksum="sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855" ftype="vcf" />
+            <output name="ggr" checksum="sha256:9e91807a25a9549070cfde5cc60844991db5cbee55d9181c61e75220b67f35c5" ftype="txt" />
+            <output name="xfma" checksum="sha256:1774759cc4c34b53e117406a9055f933620960be852ab77501eab1d34badbbfa" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        https://harvest.readthedocs.io/en/latest/content/parsnp.html
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3364789</citation>
+        <citation type="doi">10.1101/007351</citation>
+    </citations>
+</tool>