Mercurial > repos > nml > srst2
diff srst2.xml @ 1:599a4dc309aa draft
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
author | nml |
---|---|
date | Wed, 01 Mar 2017 12:39:11 -0500 |
parents | 6f870ed59b6e |
children | e59fdf6145db |
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--- a/srst2.xml Mon Feb 06 12:31:04 2017 -0500 +++ b/srst2.xml Wed Mar 01 12:39:11 2017 -0500 @@ -1,16 +1,13 @@ -<tool id="srst2" name="SRST2" version="0.3.6"> +<tool id="srst2" name="SRST2" version="0.3.7"> <description>Short Read Sequence Typing for Bacterial Pathogens</description> <requirements> - <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> <requirement type="package" version="0.1.4.6">srst2</requirement> - <requirement type="package" version="08-07-2014">vfdb</requirement> </requirements> <stdio> - <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> + <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> </stdio> - <command interpreter="perl"> - srst2.pl \$BASE/srst2.py $bam_results $scores $pileup + <command><![CDATA[ + $__tool_directory__/srst2.pl $bam_results $scores $pileup #if $mlst_or_genedb.job_type == "mlst_only" m $txt_results $alleles @@ -21,10 +18,10 @@ #end if #else if $mlst_or_genedb.job_type == "custom_only" g $genes_results $fullgenes_results - #* - to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed - make the database names an array and then join - *# + #* + to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed + make the database names an array and then join + *# #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) "$dbs" #else if $mlst_or_genedb.job_type == "vfdb_only" @@ -121,15 +118,15 @@ --other "'-p \${GALAXY_SLOTS:-1}'" #end if - --output out - </command> + --output \${PWD}/out + ]]></command> <inputs> <conditional name="single_or_paired"> <param name="type" type="select" label="Read type"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> <option value="collection">Collection Paired-end</option> - </param> + </param> <when value="single"> <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> </when> @@ -138,7 +135,7 @@ <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> </when> <when value="collection"> - <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" /> + <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" /> </when> </conditional> @@ -170,7 +167,7 @@ <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> <param name="vfdb_in" type="select" label="Choose a VFDB strain"> - <options from_data_table="vfdb_fasta_files" /> + <options from_data_table="vfdb_fasta_files" /> </param> <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value="" help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/> @@ -252,9 +249,26 @@ </outputs> <tests> - <test> - <output/> - </test> + <test> + <param name="type" value="collection" /> + <param name="fastq_collection"> + <collection type="paired"> + <element name="forward" value="ERR028678_sampled_1.fastq" /> + <element name="reverse" value="ERR028678_sampled_2.fastq" /> + </collection> + </param> + <param name="job_type" value="mlst_only" /> + <param name="mlst_defs" value="ecoli.txt" /> + <param name="mlst_db" value="Escherichia_coli#1.fasta" /> + <param name="mlst_max_mismatch" value="10" /> + <param name="mlst_delim" value="-" /> + <output name="bam_results" file="ERR028678_sampled.bam" ftype="bam" lines_diff="2" /> + <output name="scores" file="ERR028678_sampled_scores.tabular" /> + <!-- Don't test pileup as it is too large of a file > 90 MB --> + <!-- <output name="pileup" file="ERR028678_sampled_pileup.tabular" />--> + <output name="alleles" file="ERR028678_sampled_alleles.fasta" /> + <output name="txt_results" file="ERR028678_sampled_text_results.tabular" /> + </test> </tests> @@ -371,6 +385,8 @@ Mark Iskander + Eric Enns + </help> <citations> <citation type="doi">10.1128/AAC.01310-13</citation>