unicycler: unicycler.xml comparison

comparison unicycler.xml @ 4:2db911a4efc5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad

author	iuc
date	Thu, 06 Sep 2018 10:59:26 -0400
parents	c4eac0c7e542
children	23300b42ca18

comparison

equal deleted inserted replaced

-:c4eac0c7e542
+:2db911a4efc5
 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0">
 <macros>
-<token name="@VERSION@">0.4.4</token>
+<token name="@VERSION@">0.4.6</token>
 </macros>
 <requirements>
 <requirement type="package" version="@VERSION@">unicycler</requirement>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[
 ## Preparing files
 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
 ## Running Unicycler
 unicycler -t "\${GALAXY_SLOTS:-4}"
 -o ./
 --verbosity 3
 --pilon_path \$pilon
-#if str( $paired_unpaired.fastq_input_selector ) != "single"
+#if str( $paired_unpaired.fastq_input_selector ) == "paired"
 -1 '$fq1'
 -2 '$fq2'
-#else
+#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
+-1 '$fq1'
+-2 '$fq2'
+#elif str( $paired_unpaired.fastq_input_selector ) == "single"
 -s '$fq'
 #end if
 #if $long
 -l $lr
 #end if
 ## General Unicycler Options section
 ## ----------------------------------------------------------
 --mode '$mode'
 --min_fasta_length '$min_fasta_length'
 --linear_seqs '$linear_seqs'
+#if str($min_anchor_seg_len) != ''
+--min_anchor_seg_len '$min_anchor_seg_len'
+#end if
 ## Spades Options section
 ## ----------------------------------------------------------
 $spades.no_correct
 --min_kmer_frac '$spades.min_kmer_frac'
 --max_kmer_frac '$spades.max_kmer_frac'
+#if str($spades.kmers) != ''
+--kmers '$spades.kmers'
+#end if
 --kmer_count '$spades.kmer_count'
 --depth_filter '$spades.depth_filter'
 ## Rotation Options section
 ## ----------------------------------------------------------
 $rotation.no_rotate
 #end if
 --scores '${lr_align.scores}'
 #if str($lr_align.low_score) != ''
 --low_score '$lr_align.low_score'
 #end if
-## Miniasm requires racon, which is not available for python 3.x
---no_miniasm
 ]]></command>
 <inputs>
 <conditional name="paired_unpaired">
 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
 <option selected="True" value="paired">Paired</option>
 <option value="paired_collection">Paired Collection</option>
 <option value="single">Single</option>
+<option value="none">None</option>
 </param>
 <when value="paired">
 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
 </when>
 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
 </when>
 <when value="single">
 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
 </when>
+<when value="none">
+</when>
 </conditional>
 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
 <param argument="--mode" type="select" label="Select Bridging mode">
 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
 </param>
 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
+<param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
+<param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated">
+<validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator>
+</param>
 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
 </section>
 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
 <assert_contents>
 <has_text text="length=5386" />
 </assert_contents>
 </output>
 </test>
+<test>
+<conditional name="paired_unpaired">
+<param name="fastq_input_selector" value="none"/>
+</conditional>
+<param name="min_anchor_seg_len" value="10"/>
+<section name="spades">
+<param name="kmers" value="21,23"/>
+</section>
+<param name="long" value="only_long.fasta" ftype="fasta" />
+<output name="assembly_graph" ftype="txt">
+<assert_contents>
+<has_text text="S" />
+</assert_contents>
+</output>
+<output name="assembly" ftype="fasta">
+<assert_contents>
+<has_text text=">1" />
+</assert_contents>
+</output>
+</test>
 </tests>
 <help><![CDATA[
 **Unicycler**
 (default: 0.95)
 --kmer_count KMER_COUNT
 Number of k-mer steps to use in
 SPAdes assembly (default: 10)
 --depth_filter DEPTH_FILTER
 Filter out contigs lower than this fraction
 of the chromosomal depth, if doing so does
 not result in graph dead ends (default: 0.25)
 ----
 **Rotation options**

Mercurial > repos > iuc > unicycler

comparison unicycler.xml @ 4:2db911a4efc5 draft