diff unicycler.xml @ 4:2db911a4efc5 draft

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

--- a/unicycler.xml	Fri Feb 02 04:58:08 2018 -0500
+++ b/unicycler.xml	Thu Sep 06 10:59:26 2018 -0400
@@ -1,9 +1,9 @@
 <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>
+        <requirement type="package" version="@VERSION@">unicycler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ## Preparing files
@@ -58,10 +58,13 @@
 -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 $long
@@ -72,11 +75,17 @@
 --mode '$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 '$spades.depth_filter'
 ## Rotation Options section
@@ -106,8 +115,6 @@
 #if str($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">
@@ -115,6 +122,7 @@
                 <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"/>
@@ -126,6 +134,8 @@
             <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">
@@ -135,10 +145,14 @@
         </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>
@@ -312,6 +326,26 @@
                 </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[
 
@@ -434,8 +468,8 @@
         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 
+        Filter out contigs lower than this fraction
+        of the chromosomal depth, if doing so does
         not result in graph dead ends (default: 0.25)
 
 ----