diff poretools_extract.xml @ 0:7593f94691fb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/poretools_extract.xml	Tue Dec 19 14:46:31 2017 -0500
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<tool id="poretools_extract" name="Extract reads" version="@VERSION@.0">
+    <description>in FASTA or FASTQ format from nanopore files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+        poretools $output_format --type $type --min-length $min_length --max-length $max_length
+        $quality
+        #if $group:
+            --group '$group'
+        #end if
+        #if $start:
+            --start '$start'
+        #end if
+        #if $end:
+            --end '$end'
+        #end if
+        '$input' > '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
+        <param name="output_format" type="select" label="Output format">
+            <option value="fastq">FASTQ</option>
+            <option value="fasta">FASTA</option>
+        </param>
+        <expand macro="length_options" />
+        <param argument="--type" type="select" label="FASTQ Type">
+            <option value="all">All</option>
+            <option value="fwd">Forward</option>
+            <option value="rev">Reverse</option>
+            <option value="2D">2D</option>
+            <option value="fwd,rev">Forward and reverse</option>
+            <option value="best">Best</option>
+        </param>
+        <param name="quality" type="select" label="Filter by complement events">
+            <option value="">Do not filter</option>
+            <option value="--high-quality">Only report reads with more</option>
+            <option value="--normal-quality">Only report reads with fewer</option>
+        </param>
+        <param argument="--group" type="integer" optional="True" label="Base calling group serial number to extract" />
+        <param argument="--start" type="integer" optional="True" label="Start timestamp" />
+        <param argument="--end" type="integer" optional="True" label="End timestamp" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fastq">
+            <change_format>
+                <when input="output_format" value="fasta" format="fasta" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="test_input" />
+            <param name="output_format" value="fastq" />
+            <output name="output" file="poretools-extract-out1.fastq" ftype="fastq" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="output_format" value="fasta" />
+            <output name="output" file="poretools-extract-out1.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+        Extract sequences from fast5 files generated by the Oxford Nanopore sequencing technology.
+    </help>
+    <expand macro="citations" />
+</tool>