Mercurial > repos > peterjc > samtools_depad
changeset 9:81b90fa846c7 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 12:48:01 -0400 |
| parents | 41c56cd5e2ba |
| children | 0ff1f6fd73bc |
| files | tools/samtools_depad/README.rst tools/samtools_depad/samtools_depad.py tools/samtools_depad/samtools_depad.xml |
| diffstat | 3 files changed, 14 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/samtools_depad/README.rst Wed May 10 12:47:37 2017 -0400 +++ b/tools/samtools_depad/README.rst Thu May 11 12:48:01 2017 -0400 @@ -1,14 +1,14 @@ Galaxy wrapper for samtools depad ================================= -This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2014-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This is a wrapper for part of the command line samtools suite, v0.1.19 This wrapper is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats +http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad Automated Installation @@ -54,6 +54,8 @@ - Removed unused imports from Python wrapper script. v0.0.3 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.4 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/samtools_depad/samtools_depad.py Wed May 10 12:47:37 2017 -0400 +++ b/tools/samtools_depad/samtools_depad.py Thu May 11 12:48:01 2017 -0400 @@ -15,7 +15,7 @@ if "-v" in sys.argv or "--version" in sys.argv: # Galaxy seems to invert the order of the two lines - print "(Galaxy wrapper v0.0.2)" + print "(Galaxy wrapper v0.0.4)" cmd = "samtools 2>&1 | grep -i ^Version" sys.exit(os.system(cmd)) @@ -33,9 +33,9 @@ # Run samtools depad: if input_format.lower() == "sam": - cmd = "samtools depad -S -T %s %s > %s" % (padded_ref, bam_filename, output_filename) + cmd = "samtools depad -S -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename) else: - cmd = "samtools depad -T %s %s > %s" % (padded_ref, bam_filename, output_filename) + cmd = "samtools depad -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename) return_code = os.system(cmd) if return_code:
--- a/tools/samtools_depad/samtools_depad.xml Wed May 10 12:47:37 2017 -0400 +++ b/tools/samtools_depad/samtools_depad.xml Thu May 11 12:48:01 2017 -0400 @@ -1,15 +1,14 @@ -<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.3"> +<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.4"> <description>samtools depad</description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">samtools_depad.py --version</version_command> - <command interpreter="python">samtools_depad.py "$padded_ref" "$input_bam" "$input_bam.ext" "$output_bam"</command> + <version_command> +python $__tool_directory__/samtools_depad.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/samtools_depad.py '$padded_ref' '$input_bam' '$input_bam.ext' '$output_bam' + </command> <inputs> <param name="padded_ref" type="data" format="fasta" label="Padded FASTA file (with gap characters)" /> <param name="input_bam" type="data" format="sam,bam" label="Input SAM or BAM file (mapped against the padded FASTA)" />