diff raven.xml @ 0:33b7d8481a76 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raven.xml	Wed Nov 18 19:42:15 2020 +0000
@@ -0,0 +1,99 @@
+<?xml version="1.0"?>
+<tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+    <description>De novo assembly of Oxford Nanopore Technologies data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+
+    <expand macro="version_command"/>
+
+<!--TODO in future version : enable CUDA support for racon polishing-->
+
+    <command detect_errors="exit_code"><![CDATA[
+#if $input_reads.is_of_type("fasta")
+    ln -s '$input_reads' ./input.fa &&
+    #set input = "input.fa"
+#elif $input_reads.is_of_type("fasta.gz")
+    ln -s '$input_reads' ./input.fa.gz &&
+    #set input = "input.fa.gz"
+#elif $input_reads.is_of_type("fastq")
+    ln -s '$input_reads' ./input.fq &&
+    #set input = "input.fq"
+#elif $input_reads.is_of_type("fastq.gz")
+    ln -s '$input_reads' ./input.fq.gz &&
+    #set input = "input.fq.gz"
+#end if
+raven 
+$weaken
+--polishing-rounds '$polishing_rounds'
+--match '$match'
+--mismatch '$mismatch'
+--gap '$gap'
+$graphical_fragment_assembly
+--disable-checkpoints
+-t \${GALAXY_SLOTS:-4}
+'$input'
+> '$out_fasta'
+    ]]></command>
+    <inputs>
+        <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/>
+        <param argument="--weaken" type="boolean" truevalue="--weaken" falsevalue="" label="use larger (k, w); (for use in assembling highly accurate sequences)" checked="false"/>
+        <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
+        <param argument="--match" type="integer" value="3"/>
+        <param argument="--mismatch" type="integer" value="-5"/>
+        <param argument="--gap" type="integer" value="-4" max="-1"/>
+        <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>
+    </inputs>
+    <outputs>
+        <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa">
+            <filter>graphical_fragment_assembly</filter>
+        </data>
+        <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
+            <output name="out_gfa" file="raven_gfa_assembly.txt">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+            <output name="out_fasta" file="raven_assembly.fasta">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
+            <param name="graphical_fragment_assembly" value="false"/>
+            <output name="out_fasta" file="raven_assembly.fasta">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+**Input**
+- fasta / fastq / fasta.gz / fastq.gz data
+
+**Output**
+
+- Assembled genome (FASTA)
+- Graphical fragment assembly (optional) (.txt)
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>