diff flye.xml @ 0:2bdeb8d42117 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 0b1a602e21fbf8cfeba1294b6b985f1fba75afe9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flye.xml	Thu Apr 04 11:08:04 2019 -0400
@@ -0,0 +1,125 @@
+<tool id="flye" name="Flye assembler" version="2.4.1">
+    <description>of long and error-prone reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>flye --version</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+
+    #for $counter, $input in enumerate($inputs):
+
+        #if $input.is_of_type('fastqsanger', 'fastq'):
+            #set $ext = 'fastq'
+        #elif $input.is_of_type('fastqsanger.gz'):
+            #set $ext = 'fastq.gz'
+        #elif $input.is_of_type('fasta.gz'):
+            #set $ext = 'fasta.gz'
+        #elif $input.is_of_type('fasta'):
+            #set $ext = 'fasta'
+        #end if
+        ln -s '$input' ./input_${counter}.${ext} &&
+    #end for
+
+    flye
+    $mode
+    #for $counter, $input in enumerate($inputs):
+        ./input_${counter}.$ext
+    #end for
+
+    -o out_dir
+    -g '$g'
+    -t \${GALAXY_SLOTS:-4}
+    -i $i
+    #if $m:
+        -m '$m'
+    #end if
+    #if $asm-coverage:
+        --asm-coverage '$asm-coverage'
+    #end if
+    #if $plasmid:
+        '$plasmid'
+    #end if
+    #if $meta:
+        '$meta'
+    #end if
+    #if $no-trestle:
+        '$no-trestle'
+    #end if
+    2>&1
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
+        <param name="mode" type="select" label="Mode">
+            <option value="--nano-raw">Nanopore raw</option>
+            <option value="--nano-corr">Nanopore corrected</option>
+            <option value="--pacbio-raw">PacBio raw</option>
+            <option value="--pacbio-corr">PacBio corrected</option>
+            <option value="--subassemblies">high-quality contig-like input</option>
+        </param>
+        <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
+            <validator type="regex" message="Genome size must be a float  or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
+        </param>
+        <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
+        <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
+        <param argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial contig assembly (default: not set)" />
+        <param argument="--plasmid" type="boolean" truevalue="--plasmid" falsevalue="" checked="False" label="rescue short unassmebled plasmids" />
+        <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="metagenome / uneven coverage mode" />
+        <param argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip Trestle stage" />
+    </inputs>
+    <outputs>
+        <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
+        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
+        <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/>
+        <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/>
+        <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
+            <param name="mode" value="--pacbio-raw"/>
+            <param name="g" value="10000"/>
+            <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
+            <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+            <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
+            <param name="mode" value="--nano-raw"/>
+            <param name="g" value="10000"/>
+            <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
+            <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+            <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
+            <param name="mode" value="--pacbio-raw"/>
+            <param name="g" value="10000"/>
+            <param name="i" value="2"/>
+            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
+            <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Input reads could be in FASTA or FASTQ format, uncompressed
+or compressed with gz. Currenlty, raw and corrected reads
+from PacBio and ONT are supported. The expected error rates are
+<30% for raw and <2% for corrected reads. Additionally,
+--subassemblies option performs a consensus assembly of multiple
+sets of high-quality contigs. You may specify multiple
+files with reads (separated by spaces). Mixing different read
+types is not yet supported.
+
+You must provide an estimate of the genome size as input,
+which is used for solid k-mers selection. The estimate could
+be rough (e.g. withing 0.5x-2x range) and does not affect
+the other assembly stages. Standard size modificators are
+supported (e.g. 5m or 2.6g).
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>