diff genomescope.xml @ 0:b2f674562a18 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope commit aa87b7b1713b749328c5a710f32631aab2acaa3a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genomescope.xml	Fri Apr 30 20:21:25 2021 +0000
@@ -0,0 +1,123 @@
+<tool id="genomescope" name="GenomeScope" version="@VERSION@" profile="20.01">
+    <description>Analyze unassembled short reads</description>
+    <macros>
+        <token name="@VERSION@">2.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">genomescope2</requirement>
+    </requirements>
+    <version_command>genomescope2 --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        genomescope2
+            --input '$input'
+            --output .
+            --kmer_length $kmer_length 
+            $no_unique_sequence $testing $trace_flag
+            #if $ploidy:
+                --ploidy $ploidy
+            #end if
+            #if $lambda:
+                --lambda $lambda
+            #end if
+            #if $max_kmercov:
+                --max_kmercov $max_kmercov
+            #end if
+            #if $topology:
+                --topology $topology
+            #end if
+            #if $initial_repetitiveness:
+                --initial_repetitiveness $initial_repetitiveness
+            #end if
+            #if $initial_heterozygosities:
+                --initial_heterozygosities $initial_heterozygosities
+            #end if
+            #if $transform_exp:
+                --transform_exp $transform_exp
+            #end if
+            #if $true_params:
+                --true_params $true_params
+            #end if
+            #if $num_rounds:
+                --num_rounds $num_rounds
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="Input histogram file" help="This file is a two column tabular file for example generated with the histo function of Jellyfish."/>
+        <param name="model_output" type="boolean" label="Add the model parameters to your history"/>
+        <param name="summary_output" type="boolean" label="Output a summary of the analysis"/>
+        <param name="progress_output" type="boolean" label="Additional information for each optimization round"/>
+        <param argument="--ploidy" type="integer" optional="true" label="Ploidy for model to use" help="Default: 2"/>
+        <param argument="--kmer_length" type="integer" value="21" optional="false" label="K-mer length used to calculate k-mer spectra"/>
+        <param argument="--lambda" type="integer" optional="true" label="Optional initial kmercov estimate for model to use"/>
+        <param argument="--max_kmercov" type="integer" optional="true" label="Optional maximum k-mer coverage threshold" help="K-mers with coverage greater than max_kmercov are ignored by the model"/>
+        <param argument="--no_unique_sequence" type="boolean" truevalue="--no_unique_sequence" falsevalue="" label="Turn off yellow unique sequence line in plots"/>
+        <param argument="--topology" type="integer" optional="true" label="Flag for topology for model to use"/>
+        <param argument="--initial_repetitiveness" type="integer" optional="true" label="Initial value for repetitiveness"/>
+        <param argument="--initial_heterozygosities" type="integer" optional="true" label="Initial values for nucleotide heterozygosity rates"/>
+        <param argument="--transform_exp" type="integer" optional="true" label="Parameter for the exponent when fitting a transformed (x**transform_exp*y vs. x) k-mer histogram" help="Default: 1"/>
+        <param argument="--testing" type="boolean" truevalue="--testing" falsevalue="" label="Create testing.tsv file with model parameters"/>
+        <param argument="--true_params" type="integer" optional="true" label="Flag to state true simulated parameters for testing mode"/>
+        <param argument="--trace_flag" type="boolean" truevalue="--trace_flag" falsevalue="" label="Turn on printing of iteration progress of nlsLM function"/>
+        <param argument="--num_rounds" type="integer" min="1" optional="true" label="Number of optimization rounds"/>
+    </inputs>
+    <outputs>
+        <data name="linear_plot" format="png" from_work_dir="linear_plot.png" label="${tool.name} on ${on_string} Linear plot"/>
+        <data name="log_plot" format="png" from_work_dir="log_plot.png" label="${tool.name} on ${on_string} Log plot"/>
+        <data name="transformed_linear_plot" format="png" from_work_dir="transformed_linear_plot.png" label="${tool.name} on ${on_string} Transformed linear plot"/>
+        <data name="transformed_log_plot" format="png" from_work_dir="transformed_log_plot.png" label="${tool.name} on ${on_string} Transformed log plot"/>
+        <data name="model" format="txt" from_work_dir="model.txt" label="${tool.name} on ${on_string} Model">
+            <filter>model_output</filter>
+        </data>
+        <data name="summary" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string} Summary">
+            <filter>summary_output</filter>
+        </data>
+        <data name="progress" format="txt" from_work_dir="progress.txt" label="${tool.name} on ${on_string} Progress">
+            <filter>progress_output</filter>
+        </data>
+        <data name="model_params" format="tabular" from_work_dir="SIMULATED_testing.tsv" label="${tool.name} on ${on_string} Model parameters">
+            <filter>testing</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="8">
+            <param name="input" value="genomescope-in1.tab"/>
+            <param name="kmer_length" value="21"/>
+            <param name="testing" value="true"/>
+            <param name="model_output" value="true"/>
+            <param name="summary_output" value="true"/>
+            <param name="progress_output" value="true"/>
+            <output name="linear_plot" file="genomescope-out1-1.png" ftype="png"/>
+            <output name="log_plot" file="genomescope-out1-2.png" ftype="png"/>
+            <output name="transformed_linear_plot" file="genomescope-out1-3.png" ftype="png"/>
+            <output name="transformed_log_plot" file="genomescope-out1-4.png" ftype="png" compare="sim_size"/>
+            <output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/>
+            <output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/>
+            <output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/>
+            <output name="testing" file="genomescope-out1-1.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+GenomeScope 2.0: Reference-free profiling of polyploid genomes
+==============================================================
+
+GenomeScope 2.0 applies classical insights from combinatorial theory to establish
+a detailed mathematical model of how k-mer frequencies will be distributed in
+heterozygous and polyploid genomes. GenomeScope 2.0 employs a polyploid-aware
+mixture model that, within seconds, accurately infers genome properties from
+unassembled sequencing data. GenomeScope 2.0 uses the k-mer count distribution,
+e.g. from KMC or Jellyfish, and produces a report and several informative plots
+describing the genome properties. We validate the approach on simulated polyploid
+data created using a generative model with parameters for genome size, heterozygosity,
+repetitiveness, ploidy, and sequencing coverage, and find GenomeScope 2.0 retains
+accuracy across a broad range of realistic and extreme parameter values. We also
+validate GenomeScope 2.0 by analyzing genuine sequence data from 11 diverse
+polyploid genomes with known genome characteristics.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btx153</citation>
+        <citation type="doi">10.1038/s41467-020-14998-3</citation>
+    </citations>
+</tool>