diff drep_dereplicate.xml @ 0:b59ae99e47d4 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/drep_dereplicate.xml	Mon Jan 06 11:11:06 2020 -0500
@@ -0,0 +1,66 @@
+<tool id="drep_dereplicate" name="dRep dereplicate" version="@VERSION@.0" python_template_version="3.5">
+    <description>De-replicate a list of genomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+         @PREPARE_GENOMES@
+         dRep dereplicate outdir
+         @FILTER_OPTIONS@
+         @GENOME_COMPARISON_OPTIONS@
+         @CLUSTERING_OPTIONS@
+         @SCORING_OPTIONS@
+         @TAXONOMY_OPTIONS@
+         @WARNING_OPTIONS@        
+         @GENOMES@
+    ]]></command>
+    <inputs>
+        <expand macro="genomes"/>
+        <expand macro="filtering_options"/>
+        <expand macro="genome_comparison_options"/>
+        <expand macro="clustering_options"/>
+        <expand macro="scoring_options"/>
+        <expand macro="taxonomy_options"/>
+        <expand macro="warning_options"/>
+    </inputs>
+    <outputs>
+        <expand macro="common_outputs" />
+        <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
+             <discover_datasets pattern="__designation__" directory="out_drep/dereplicated_genomes" ext='fasta'/>
+        </collection>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+
+usage: drep dereplicate [-p PROCESSORS] [-d] [-h] [-l LENGTH]
+                        [-comp COMPLETENESS] [-con CONTAMINATION]
+                        [--ignoreGenomeQuality] [-ms MASH_SKETCH]
+                        [--S_algorithm {goANI,ANIn,ANImf,gANI}]
+                        [-n_PRESET {normal,tight}] [-pa P_ANI] [-sa S_ANI]
+                        [--SkipMash] [--SkipSecondary] [-nc COV_THRESH]
+                        [-cm {total,larger}] [--clusterAlg CLUSTERALG]
+                        [-comW COMPLETENESS_WEIGHT]
+                        [-conW CONTAMINATION_WEIGHT]
+                        [-strW STRAIN_HETEROGENEITY_WEIGHT] [-N50W N50_WEIGHT]
+                        [-sizeW SIZE_WEIGHT] [--run_tax]
+                        [--tax_method {percent,max}] [-per PERCENT]
+                        [--cent_index CENT_INDEX] [--warn_dist WARN_DIST]
+                        [--warn_sim WARN_SIM] [--warn_aln WARN_ALN]
+                        [-g [GENOMES [GENOMES ...]]]
+                        [--checkM_method {taxonomy_wf,lineage_wf}]
+                        [--genomeInfo GENOMEINFO]
+                        work_directory
+
+    @GENOMES_HELP@
+    @FILTERING_HELP@
+    @GENOME_COMPARISON_HELP@
+    @CLUSTERING_HELP@
+    @SCORING_HELP@
+    @TAXONOMY_HELP@
+    @WARNINGS_HELP@
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>