diff flye.xml @ 13:0a59ae153827 draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/flye commit 98d55b7009fa22312b117a0138a17e2037d0cdb3-dirty"

--- a/flye.xml	Tue Mar 31 20:35:43 2020 +0000
+++ b/flye.xml	Thu Aug 06 13:42:00 2020 +0000
@@ -1,14 +1,15 @@
-<tool id="flye" name="Flye assembler" version="@VERSION@+galaxy1">
+<tool id="flye" name="Flye assembler" version="2.8">
     <description>of long and error-prone reads</description>
     <macros>
-        <token name="@VERSION@">2.7</token>
+        <import>macros.xml</import>
     </macros>
-    <requirements>
-    <requirement type="package" version="@VERSION@">flye</requirement>
-    </requirements>
+    <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'):
@@ -22,12 +23,19 @@
         #elif $input.is_of_type('fasta'):
             #set $ext = 'fasta'
         #end if
-        ln -s '$input' ./input.${ext} &&
+        ln -s '$input' ./input_${counter}.${ext} &&
+    #end for
+
     flye
     $mode
-    ./input.$ext
+    #for $counter, $input in enumerate($inputs):
+        ./input_${counter}.$ext
+    #end for
+
     -o out_dir
-    -g '$g'
+    #if $g:
+        -g '$g'
+    #end if    
     -t \${GALAXY_SLOTS:-4}
     -i $i
     #if $m:
@@ -37,17 +45,18 @@
         --asm-coverage '$asm_coverage'
     #end if
     #if $plasmid:
-        $plasmid
+        '$plasmid'
     #end if
     #if $meta:
-        $meta
+        '$meta'
     #end if
-    $keep_haplotypes
-    $trestle
+    #if $no_trestle:
+        '$no_trestle'
+    #end if
     2>&1
     ]]>    </command>
     <inputs>
-        <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="false" label="Input reads">
+        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads">
             <help><![CDATA[
 
     Input reads could be in FASTA or FASTQ format, uncompressed
@@ -67,17 +76,19 @@
             <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)">
+        <param argument="-g" optional="true" type="text" label="estimated genome size (for example, 5m or 2.6g)">
             <help>
                 <![CDATA[
+                <span>Since version 2.8, no longer required as input. However, it must be used in conjunction with --asm-coverage option. </span>
+                <br>
             <span>The genome size estimate is used for solid k-mer selection in the
             initial disjointig assembly stage. <b>Flye is not very sensitive to this
             parameter, and the estimate could be rough</b>. It is ok if the parameter is
             within 0.5x-2x of the actual genome size. If the final assembly size is
             very different from the initial guess, consider re-running the pipeline
             with an updated estimate for better results.</span>
-<br>
-<span>An alternative option is to run Flye in <b>--meta</b> mode, which uses a different
+            <br>
+            <span>An alternative option is to run Flye in <b>--meta</b> mode, which uses a different
             approach for solid k-mer selection. This mode is almost independent from the
             genome size parameter (you still need to provide an estimate for the selection
             of some other parameters). When assembly is completed, you can re-run in the
@@ -91,15 +102,14 @@
         <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="--keep_haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Do not collapse alternative haplotypes"/>
-        <param argument="--trestle" type="boolean" truevalue="--trestle" falsevalue="" checked="False" label="Enable Trestle" help="After resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies"/>
+        <param argument="--no_trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip Trestle stage" help="After resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies"/>
     </inputs>
     <outputs>
+        <data name="assembly" format="fasta" from_work_dir="out_dir/assembly.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 ${on_string} (log)"/>
-        <data name="scaffolds" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
     </outputs>
     <tests>
         <test>
@@ -163,8 +173,5 @@
     scaffolds.fasta file is a symlink to assembly.fasta, which is retained for the backward compatibility.
     ]]>
     </help>
-    <citations>
-        <citation type="doi">10.1073/pnas.1604560113</citation>
-        <citation type="doi">10.1038/s41587-019-0072-8</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>