diff mapsembler2.xml @ 0:265fa5effd4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapsembler2.xml	Fri Oct 20 03:15:10 2017 -0400
@@ -0,0 +1,110 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool profile="16.04" id="mapsembler2" name="Mapsembler2" version="2.2.4">
+    <description>is a targeted assembly software</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.2.4">mapsembler2</requirement>
+    </requirements>
+    <command><![CDATA[
+
+        #set $starter_filename = str($s) + "." + $s.ext
+        ln -sf '${s}' '${starter_filename}' &&
+
+        #set $samples = []
+        #for $read in $r
+            #set $filename = str($read) + "." + $read.ext
+            ln -sf '${read}' '${filename}' &&
+            #silent $samples.append($filename)
+        #end for
+
+        run_mapsembler2_pipeline.sh
+        -s '${starter_filename}'
+        -r "${ ' '.join(['%s' % read for read in $samples]) }"
+        -t ${t}
+        -k ${k}
+        -c ${c}
+        -d ${d}
+        -g ${g}
+        -f ${f}
+        -x ${x}
+        -y ${y}
+    ]]></command>
+
+    <inputs>
+        <!-- Input data files -->
+        <param argument="-s" type="data" format="fasta" label="Starters" help="Set of input sequences" />
+        <param argument="-r" type="data" multiple="true" format="fasta,fastq" label="List of reads" />
+        <param argument="-t" type="select" label="Select your output extension type">
+            <option value="1">a strict sequence</option>
+            <option value="2">a consensus sequence</option>
+        </param>
+        <param argument="-k" type="integer" label="Size of kmers" value="31" help="Set the length of used kmers. Must fit the compiled value. Only uneven number" />
+        <param argument="-c" type="integer" label="Minimal coverage" value="5" help="Set the minimal coverage: Used by Phaser (don't use kmers with lower coverage) "/>
+        <param argument="-d" type="integer" label="Number of authorized substitutions" value="1" help="Set the number of authorized substitutions used while mapping reads on finding SNPs"/>
+        <param argument="-g" type="integer" label="Estimated genome size" value="10000000" help="Used only to control memory usage. e.g.3 billion (3000000000) uses 4Gb of RAM." />
+        <param argument="-f" type="select" label="Process of search" help="Set the process of search in the graph" >
+            <option value="1">Breadth</option>
+            <option value="2">Depth</option>
+        </param>
+        <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/>
+        <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
+    </inputs>
+
+    <outputs>
+        <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/>
+        <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="Coherent with ${tool.name} on $on_string" hidden="true"/>
+        <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="Uncoherent with ${tool.name} on $on_string" hidden="true"/>
+        <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="s" value="mapsembler2/starter.fa" />
+            <param name="r" value="mapsembler2/reads1,mapsembler2/reads2" />
+            <param name="t" value="2"/>
+            <output name="fasta" file="mapsembler2/assembly.fa"/>
+        </test>
+        <test>
+            <param name="s" value="mapsembler2/starter.fa" />
+            <param name="r" value="mapsembler2/reads2,mapsembler2/reads1" />
+            <param name="t" value="1"/>
+            <output name="fasta" file="mapsembler2/assembly_2.fa"/>
+            <output name="coherent" file="mapsembler2/coherent.fa"/>
+            <output name="extremities" file="mapsembler2/starter_extremities.fa"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**Description**
+
+Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
+Mapsembler2 may be used for (not limited to):
+
+· Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
+
+· Checks if a gene (input as starter) has an homolog in a set of reads.
+
+· Checks if a known enzyme is present in a metagenomic NGS read set.
+
+· Enrich unmappable reads by extending them, possibly making them mappable.
+
+· Checks what happens at the extremities of a contig.
+
+· Remove contaminants or symbiont reads from a read set
+
+-------
+
+**Web site**
+
+http://colibread.inria.fr/mapsembler2/
+
+
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1471-2105-13-48</citation>
+    </expand>
+
+</tool>