diff artic_guppyplex.xml @ 0:7a82006f7c05 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/artic_guppyplex.xml	Fri Aug 27 20:34:52 2021 +0000
@@ -0,0 +1,50 @@
+<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy0" profile="20.09">
+    <description>Filter Nanopore reads by read length and (optionally) quality</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        mkdir inputs &&
+        #for $i, $elem in enumerate($input)
+            ln -fs '$elem' inputs/fastq${i}.fastq &&
+        #end for
+        artic guppyplex --min-length $min_length --max-length $max_length
+            --directory inputs/
+            --prefix artic_guppyplex --output '$output1'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" />
+        <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" />
+        <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" />
+        <param name="skip_quality_check" argument="--skip-quality-check" type="boolean" truevalue="--skip-quality-check" falsevalue="" checked="False" label="Do not filter on quality score (speeds up processing)" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="fastq" from_work_dir="run_name_.fastq" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test.fastq" />
+            <output name="output1" file="gupplyplex_output.fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        The ARTIC_ guppyplex tool filters reads by length and (optionally) quality.
+        This filter is typically used as a pre-processing step in the processing
+        of amplicon sequencing Nanopore reads, where a size-based filter can
+        be used to remove possibly-chimeric reads.
+        
+        The default paramters of the tool (minimum length of 400 and maximum of 700)
+        are based on the ARTIC amplicon scheme. If used with a different amplicon
+        scheme they should be adjusted to use the minimum length of an amplicon as
+        the minimum length and the maximum length of an amplicon plus 200 as the
+        maximum length.
+
+        .. _ARTIC: https://artic.readthedocs.io/en/latest/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file