Mercurial > repos > peterjc > seq_filter_by_mapping
changeset 9:c64494ea41ea draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
| author | peterjc |
|---|---|
| date | Fri, 21 Apr 2017 12:06:34 -0400 |
| parents | 69decf35d578 |
| children | 3e1e1fbdb3d0 |
| files | tools/seq_filter_by_mapping/README.rst tools/seq_filter_by_mapping/seq_filter_by_mapping.xml tools/seq_filter_by_mapping/tool_dependencies.xml |
| diffstat | 3 files changed, 16 insertions(+), 18 deletions(-) [+] |
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--- a/tools/seq_filter_by_mapping/README.rst Thu Feb 09 11:27:06 2017 -0500 +++ b/tools/seq_filter_by_mapping/README.rst Fri Apr 21 12:06:34 2017 -0400 @@ -1,7 +1,7 @@ Galaxy tool to filter FASTA, FASTQ or SFF sequences by SAM/BAM mapping ====================================================================== -This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute +This tool 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. @@ -67,6 +67,9 @@ - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.5 - Python script cleanups (internal change only). + - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml Thu Feb 09 11:27:06 2017 -0500 +++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml Fri Apr 21 12:06:34 2017 -0400 @@ -1,28 +1,23 @@ <tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.5"> <description>from SAM/BAM file</description> <requirements> - <requirement type="package" version="1.64">biopython</requirement> - <requirement type="python-module">Bio</requirement> - <requirement type="binary">samtools</requirement> + <requirement type="package" version="1.67">biopython</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">seq_filter_by_mapping.py --version</version_command> - <command interpreter="python"> -seq_filter_by_mapping.py -i "$input_file" -f "$input_file.ext" -m $pair_mode + <version_command> +python $__tool_directory__/seq_filter_by_mapping.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/seq_filter_by_mapping.py -i '$input_file' -f '$input_file.ext' -m $pair_mode #if $output_choice_cond.output_choice=="both" - -p $output_pos -n $output_neg + -p '$output_pos' -n '$output_neg' #elif $output_choice_cond.output_choice=="pos" - -p $output_pos + -p '$output_pos' #elif $output_choice_cond.output_choice=="neg" - -n $output_neg + -n '$output_neg' #end if ## Now loop over all the mapping files -#for i in $mapping_file#${i} #end for# +#for i in $mapping_file#'${i}' #end for# </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
--- a/tools/seq_filter_by_mapping/tool_dependencies.xml Thu Feb 09 11:27:06 2017 -0500 +++ b/tools/seq_filter_by_mapping/tool_dependencies.xml Fri Apr 21 12:06:34 2017 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.64"> - <repository changeset_revision="bc1d7fa4ad08" name="package_biopython_1_64" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />