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changeset 0:f8e25d69167d draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:47:27 -0400
parents
children 0a4f83207e53
files albacore_1D.py albacore_1D.xml test-data/test_data.fast5.tar.gz test-data/test_data.fastq
diffstat 4 files changed, 178 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/albacore_1D.py	Wed Aug 30 02:47:27 2017 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+
+import sys, os
+import glob
+import tarfile
+import subprocess
+import shutil
+import h5py
+import numpy as np
+
+def main():
+    tar_file = sys.argv[1]
+    out_file = sys.argv[2]
+    threads  = sys.argv[3]
+
+    (flowcell, kit) = parse_meta(tar_file)
+
+    subprocess.call(["read_fast5_basecaller.py",
+        "--input", "in_dir",
+        "--worker_threads", threads,
+        "--save_path", "out_dir",
+        "--flowcell", flowcell,
+        "--kit", kit,
+        "--recursive",
+        "--files_per_batch_folder", "0",
+        "--output_format", "fastq",
+        "--reads_per_fastq_batch", "999999999" ])
+
+    #check for single albacore output and copy to Galaxy output
+    files = glob.glob("out_dir/workspace/*.fastq")
+    if len(files) != 1:
+        raise ValueError('No or multiple FASTQ output files found')
+    found_file = files[0]
+    shutil.copy(found_file, out_file)
+
+def parse_meta(fn):
+
+    try:
+        in_dir = "in_dir"
+        if not os.path.exists(in_dir):
+            os.makedirs(in_dir)
+
+        tar = tarfile.open(fn, mode='r')
+        tar.extractall(path=in_dir)
+
+        files = glob.glob(
+            os.path.join(in_dir, "**", "*.fast5"),
+            recursive=True
+        )
+        if len(files) < 1:
+            raise ValueError('No FAST5 files found')
+        test_file = files[0]
+
+        f = h5py.File(test_file,"r")
+        flowcell = f["/UniqueGlobalKey/context_tags"].attrs["flowcell"].upper()
+        kit = f["/UniqueGlobalKey/context_tags"].attrs["sequencing_kit"].upper()
+    except OSError as e:
+        print("Unexpected error:", e.strerror)
+        raise
+
+    except:
+        print("Unexpected error:", sys.exc_info()[0])
+        raise
+
+    return flowcell, kit
+
+if __name__ == "__main__" :
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/albacore_1D.xml	Wed Aug 30 02:47:27 2017 -0400
@@ -0,0 +1,78 @@
+<tool id="albacore_1D" name="Albacore 1D" version="1.2.6">
+
+    <description>ONT production basecaller</description>
+
+    <!-- ***************************************************************** -->
+   
+    <!--
+    <requirements>
+        <requirement type="package" version="1.2.6">albacore</requirement>
+    </requirements>
+    -->
+
+    <!-- ***************************************************************** -->
+
+    <version_command>read_fast5_basecaller.py --version | perl -wnE'print "$1\n" for /\(version ([^\)]+)\)/g'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    python3 $__tool_directory__/albacore_1D.py $input $output \${GALAXY_SLOTS:-1}
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="input" type="data" format="fast5_archive" label="Input reads" />
+
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+
+        <data name="output" format="fastq" label="${tool.name} on ${on_string} (called.fastq)" />
+
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
+            <output name="output" file="test_data.fastq" compare="diff" />
+        </test>
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+    <![CDATA[
+
+**Description**
+
+Albacore is a tool for basecalling Oxford Nanopore reads. It is distributed by
+ONT to authorized community members only and thus is not packaged through
+Galaxy or Bioconda. End users are responsible for installing and testing the
+albacore software themselves and ensuring that it is in the galaxy user $PATH.
+
+The Galaxy wrapper has modified albacore to take a gzip tarball of FAST5 reads
+as input, such as can be produced by `poretools combine`, and always outputs a
+single FASTQ file.
+
+This is the 1D basecaller.
+
+    ]]>
+    </help>
+
+    <!-- ***************************************************************** -->
+    
+    <citations>
+    </citations>
+
+</tool>
Binary file test-data/test_data.fast5.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_data.fastq	Wed Aug 30 02:47:27 2017 -0400
@@ -0,0 +1,32 @@
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+TTTTTTTTTTTTTTTTGCACTCATTTGGCCGCTAATTCGTCCGTATTGATCTAGTGACGCAGTGAGTAAGCAGGTATTTTCATCATCAAATAGTGAGCGAGGATTATATCTCGGCTCTGCTCGATGGTGGCGAGCAGGCATCGCTGACTGAAACATACCATGTGCCGATACCGCGTGAAACTGGCCGTGGCGCTTCGCTTTGTAGAACTTGCATTGAGGTATTTACCAAGACACCGTTTGCGGAGGTGATTGCTCGCACTCAGGTGCAGCCTATGCAGAAACGTGTAATTTAAGAGCTCATTAATGATATCATTAAAATTCGCGAGTGCTCGTCGAGGGGCTGATGCATTTCGACTCTCTGTGACATGTCTCAAGTGGCCGTGAAGTATCGCAGTAATATATGAAATATAATTAATGTCAGAGATTTCTGGCCGTCGAAATGCGCTAAAGTAAACAATATGATGTTAGCCGATAAAATTATTATAGTGCATTATTCTGATACTTGAAGCCTCGCTGATATTGAGGAAGTATGAAATATTATCGATATTCGACGTCATATCGATTAAATATGTCGAGAGCGAAATAGTCGTACAAGTATATCAAGGGCAACTTGCCGAATAAATGCTCGCTCTTATTTTTAAAAAAATTCGGCTGTTTCGTGGCCGGTGGTAGCACTCTTACTCTGGTAGCGGCCCATCAATCGGGCATCACTTTAAATTATCAGTCTGCCGATAATTGGCGGGCATGCGAAAACGTCTACTCGAAACCCGGCGACAGTGAATCGTAGCCTTTGTCGCACCAGCTTTTGCGACTCATAAGTATTC
++
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++
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++
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++
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++
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++
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+ATATTATGCTAAATTGGAAGTGCGTATGAATACAGAAGCTGACGCGAGAGTGAGCGAAAGCGAAATGACGAAGCATGTCAAAAATTACAACTTTAATATCGGCTAGAATGAGCTGCTAAGCATGTCGCAAGCGTGGGCCGAAACTAAAGATGATATTTGATATCATTAAGCTGGCATAGAATCAGAAAGCGGCGTAAAGTCTCGGCATCGAGCATTATAGTGCGAAAGCGGGAAATGATGAAGCGGTGAGAATACATCAAAGGCGCTCAAAGTAAATGTAGAATGCGCGATATCAATGATATATTAATGAAAGAAATATCGAAATCAGTGTATAAACGACACGGCTGGCGAATTCACTAATATCGAAATGGGCCGAGGCGGTAATGAGCCGAGCGCATCGCTGAGGCAGTATAGTGTAATCCTGATATAAATTCCAGGGCGCAATATACTCGAAGCTTTGCGAAGAGAGCGTGGAAACACAATGGCATATATGAGGGGCGTAGCAATGAGATATAAAGTAACGATGAAATTCTCATCGAGAGCTCAAATGAAATAATCGGCGCGGTCGTCCTGCCTCGAAGCCCTAAAGAGGTAATGAAGGCGAAATGATGAGGCATATCTCCCAAGCGAAAGCGAGAAAATGGAGAGCAATCAGGCCGAAGTGGCTCGGTATTGATCGAAAGTGCGCGATCGAAACGAGAGAGCGACGGGCGATCAGCCAGCGCTTGGTATAACGTAGCTCAATGGGCGAAACCGAAACACCGACAATAGTGATAAAGAAACGCGCCATTTC
++
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
+@310f7b48-a3e0-4cdc-b396-09f4b86081dd runid=d28f9f1c34b8f7416c367df1e0c4a864ba830c9c read=12113 ch=399 start_time=2017-08-09T20:02:08Z
+TCTTTCATTTGTGGCAGGTGGAGCGTATTCGAATCTCGAAACTGGCGCGGTGATGAAACTTGAGGTATTTTATCGCTAAATAATTTGGCCGAGGTTACTCGCTCAACTCTGCTTCGGCTGATAATTGAAACAATAAAGCGTCATCTGTTGACTGATGCTCTGTGTTGCTGTCGTGGCAGCGATCATTGTTCTTAGAGCTTTAGCGACAAGTGTTATAAACAAGAACAACGGAGGTAGGAATGCTCGTATGGCGGCGAAGTGTATGAATTTCATGAGAGGGCTCGACTATTGATGCAATAAAATTGCATTCGAGTCTCGTCAGGGGCTTTTGATAGCCCTGACGTCTCGTCGGTATATGAGAGAAATGGCGATGAAATTTCTCGCGATTCAACCATAACTATAAAGTACAATGGCCATCAGGTTTCGGCGTCAGTCGCTGAAAGTAAAACACCGACCATATGATATTTGTAAATGCGTTATTAACAATTCGTGCAATGCCGAGGCGCAAGCACCTGTTGGTATGGCGCATCAGGCAATCATCGATATTCTTCAATAGTCATATCGGTCGATATGGTGGCAGGCAGGCAATAGTCGTACCGAGTGGCACTCCATCGTTAACTACTCTCGAAATCGCTCATATCATTTTACGCGTCTTCTTCGTGTCCGGGCCGAAATTAGCCTGCTCTTGCATAAGAACCTGATGCGGCGCGGCCATCGAGGTCTCCGATGCTGCCGTCGTGCATGCTTGAAAACTTGTCTACTCGAAAGCTCGACGCGTGTCAAAGCTAAAATTATGTTTTTTATTGGCATATTTATCGCTT
++
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