Mercurial > repos > greg > vsnp_get_snps
changeset 10:be5875f29ea4 draft
Uploaded
author | greg |
---|---|
date | Tue, 03 Aug 2021 19:24:50 +0000 (2021-08-03) |
parents | 0fe292b20b9d |
children | fa304dc06f12 |
files | .shed.yml macros.xml vsnp_get_snps.py vsnp_get_snps.xml |
diffstat | 4 files changed, 51 insertions(+), 12 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Aug 03 19:24:50 2021 +0000 @@ -0,0 +1,11 @@ +name: vsnp_get_snps +owner: greg +description: | + Contains a tool that collects quality parsimonious SNPs from vcf files and outputs alignment files in fasta format. +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + Contains a tool that collects quality parsimonious SNPs from vcf files and outputs alignment files in fasta format. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps +type: unrestricted +categories: + - Sequence Analysis
--- a/macros.xml Thu Jul 29 13:16:03 2021 +0000 +++ b/macros.xml Tue Aug 03 19:24:50 2021 +0000 @@ -1,7 +1,34 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> <token name="@WRAPPER_VERSION@">1.0</token> - <token name="@PROFILE@">19.09</token> + <token name="@PROFILE@">20.09</token> + <xml name="biopython_requirement"> + <requirement type="package" version="1.79">biopython</requirement> + </xml> + <xml name="numpy_requirement"> + <requirement type="package" version="1.21.1">numpy</requirement> + </xml> + <xml name="openpyxl_requirement"> + <requirement type="package" version="3.0.7">openpyxl</requirement> + </xml> + <xml name="pandas_requirement"> + <requirement type="package" version="1.3.0">pandas</requirement> + </xml> + <xml name="pysam_requirement"> + <requirement type="package" version="0.15.4">pysam</requirement> + </xml> + <xml name="pyvcf_requirement"> + <requirement type="package" version="0.6.8">pyvcf</requirement> + </xml> + <xml name="pyyaml_requirement"> + <requirement type="package" version="5.4.1">pyyaml</requirement> + </xml> + <xml name="xlrd_requirement"> + <requirement type="package" version="2.0.1">xlrd</requirement> + </xml> + <xml name="xlsxwriter_requirement"> + <requirement type="package" version="1.4.4">xlsxwriter</requirement> + </xml> <xml name="param_reference_source"> <param name="reference_source" type="select" label="Choose the source for the reference genome"> <option value="cached" selected="true">locally cached</option>
--- a/vsnp_get_snps.py Thu Jul 29 13:16:03 2021 +0000 +++ b/vsnp_get_snps.py Tue Aug 03 19:24:50 2021 +0000 @@ -440,7 +440,7 @@ parser = argparse.ArgumentParser() parser.add_argument('--ac', action='store', dest='ac', type=int, help='Allele count value'), - parser.add_argument('--all_isolates', action='store_true', dest='all_isolates', required=False, default=False, help='Create table with all isolates'), + parser.add_argument('--all_isolates', action='store_true', dest='all_isolates', help='Create table with all isolates'), parser.add_argument('--input_excel', action='store', dest='input_excel', required=False, default=None, help='Optional Excel filter file'), parser.add_argument('--input_vcf_dir', action='store', dest='input_vcf_dir', help='Input vcf directory'), parser.add_argument('--min_mq', action='store', dest='min_mq', type=int, help='Minimum map quality value'),
--- a/vsnp_get_snps.xml Thu Jul 29 13:16:03 2021 +0000 +++ b/vsnp_get_snps.xml Tue Aug 03 19:24:50 2021 +0000 @@ -1,13 +1,13 @@ -<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.0+galaxy0" profile="@PROFILE@"> +<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="3.0.7">openpyxl</requirement> - <requirement type="package" version="1.3.0">pandas</requirement> - <requirement type="package" version="0.6.8">pyvcf</requirement> - <requirement type="package" version="2.0.1">xlrd</requirement> + <expand macro="openpyxl_requirement"/> + <expand macro="pandas_requirement"/> + <expand macro="pyvcf_requirement"/> + <expand macro="xlrd_requirement"/> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re @@ -27,8 +27,7 @@ #if str($dbkey) == '?': #set dbkey = $i.metadata.dbkey #else if str($dbkey) != $i.metadata.dbkey: - >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && -exit 1 + >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && exit 1 #end if #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' && @@ -49,7 +48,7 @@ #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached': #set excel_file = 'No genome specified for input VCF (database) file(s)' #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields() - ## The value of excel_fields is a nested list that looks like this. + ## The value of excel_fields is a nested list that looks like this. ## [['AF2122', 'Mbovis_define_filter.xlsx', '~/tool-data/vsnp/AF2122/excel/Mbovis_define_filter.xlsx', 'Excel file for AF2122'],...] #for $i in $excel_fields: #if str($i[0]) == $dbkey: @@ -110,7 +109,6 @@ <when value="cached"> <param name="input_excel" type="select" label="Excel file"> <options from_data_table="vsnp_excel"> - <filter type="data_meta" column="0" key="dbkey" ref="input_vcf_collection"/> <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/> </options> </param> @@ -122,7 +120,7 @@ </when> <when value="no"/> </conditional> - <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="false" label="Create a group containing all isolates?"/> + <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> </inputs> <outputs> <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)"> @@ -154,6 +152,7 @@ </collection> </param> <param name="input_excel_param" value="no"/> + <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/> </output_collection> @@ -182,6 +181,7 @@ </collection> </param> <param name="input_excel_param" value="no"/> + <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> </output_collection> @@ -211,6 +211,7 @@ </param> <param name="input_excel_param" value="yes"/> <param name="input_excel" value="89"/> + <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> </output_collection>