comparison vsnp_get_snps.xml @ 10:be5875f29ea4 draft

Uploaded

9:0fe292b20b9d

<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.0+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>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re

#set input_vcf_dir = 'input_vcf_dir'

#set dbkey = '?'
#for $i in $input_vcf_collection:
    #if str($dbkey) == '?':
        #set dbkey = $i.metadata.dbkey
    #else if str($dbkey) != $i.metadata.dbkey:
        >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" &&
exit 1
    #end if
    #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
    ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
#end for
#if str($dbkey) == '?':

#end if
#if str($input_excel_cond.input_excel_param) == 'yes':
    #if str($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.
        ## [['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:
                #set excel_file = $i[2]
                #break

                        <option value="history">from history</option>
                    </param>
                    <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>
                    </when>
                    <when value="history">

                    </when>
                </conditional>
            </when>
            <when value="no"/>
        </conditional>
        <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="false" label="Create a group containing all isolates?"/>
    </inputs>
    <outputs>
        <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)">
            <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
        </collection>

                    <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
                    <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_excel_param" value="no"/>
            <output_collection name="snps" type="list" count="1">
                <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/>
            </output_collection>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>

                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_excel_param" value="no"/>
            <output_collection name="snps" type="list" count="1">
                <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
            </output_collection>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>

                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_excel_param" value="yes"/>
            <param name="input_excel" value="89"/>
            <output_collection name="snps" type="list" count="1">
                <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/>
            </output_collection>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>

10:be5875f29ea4

<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>
        <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

#set input_vcf_dir = 'input_vcf_dir'

#set dbkey = '?'
#for $i in $input_vcf_collection:
    #if str($dbkey) == '?':
        #set dbkey = $i.metadata.dbkey
    #else if str($dbkey) != $i.metadata.dbkey:
        >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && exit 1
    #end if
    #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
    ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
#end for
#if str($dbkey) == '?':

#end if
#if str($input_excel_cond.input_excel_param) == 'yes':
    #if str($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.
        ## [['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:
                #set excel_file = $i[2]
                #break

                        <option value="history">from history</option>
                    </param>
                    <when value="cached">
                        <param name="input_excel" type="select" label="Excel file">
                            <options from_data_table="vsnp_excel">
                                <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
                            </options>
                        </param>
                    </when>
                    <when value="history">

                    </when>
                </conditional>
            </when>
            <when value="no"/>
        </conditional>
        <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)">
            <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
        </collection>

                    <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
                    <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
                </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>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>

                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
                </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>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>

                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
                </collection>
            </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>
            <output_collection name="json_avg_mq" type="list" count="1">
                <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>