# HG changeset patch
# User estrain
# Date 1511926484 18000
# Node ID 0869a76e692bdfd8aab7d40719784638603c0a37

Uploaded

diff -r 000000000000 -r 0869a76e692b srst2_fda.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srst2_fda.xml	Tue Nov 28 22:34:44 2017 -0500
@@ -0,0 +1,173 @@
+<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
+    <requirements>
+        <requirement type="package" version="0.2.0">srst2</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $paired_conditional.sPaired == "paired"
+           ln -s $paired_conditional.fastq1 sample_1.fastq;
+           ln -s $paired_conditional.fastq2 sample_2.fastq;
+        #end if
+
+        srst2
+
+        #if $paired_conditional.sPaired == "single"
+            --input_se $paired_conditional.fastq1
+        #else if $paired_conditional.sPaired == "paired"
+            --input_pe sample_1.fastq sample_2.fastq
+        #end if
+
+        --output srst2out 
+        --save_scores 
+        --mlst_definitions "$mlst_definitions" 
+        --mlst_db "$mlst_db" 
+        --mlst_delimiter $mlstdelim
+        --mlst_max_mismatch $mlst_max_mismatch
+
+    ]]></command>
+    <inputs>
+      <conditional name="paired_conditional">
+        <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
+          <option value="single">Single-end</option>
+          <option value="paired">Paired-end</option>
+        </param>
+        <when value="single">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" />
+        </when>
+        <when value="paired">
+          <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" />
+        </when>
+      </conditional>
+
+        <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
+        <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
+        <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
+        <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read for MLST allele calling (default 10)" />
+    </inputs>
+
+    <outputs>
+      <data format="txt" label="Scores" name="scores" from_work_dir="*.scores"/>
+      <data format="bam" label="bam alignment" name="bam" from_work_dir="*.sorted.bam"/>
+      <data format="pileup" label="pileup" name="pileup" from_work_dir="*.pileup"/>
+      <data format="txt" label="Alleles" name="alleles" from_work_dir="*results.txt"/>
+    </outputs>
+
+    <help><![CDATA[
+
+SRST2 - Short Read Sequence Typer (v2)
+
+This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
+
+
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --version             show program's version number and exit
+  --input_se INPUT_SE 
+                        Single end read file(s) for analysing (may be gzipped)
+  --input_pe INPUT_PE 
+                        Paired end read files for analysing (may be gzipped)
+  --merge_paired        Switch on if all the input read sets belong to a
+                        single sample, and you want to merge their data to get
+                        a single result
+  --forward FORWARD     Designator for forward reads (only used if NOT in
+                        MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise
+                        default is _1, i.e. expect forward reads as
+                        sample_1.fastq.gz)
+  --reverse REVERSE     Designator for reverse reads (only used if NOT in
+                        MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise
+                        default is _2, i.e. expect forward reads as
+                        sample_2.fastq.gz
+  --read_type READ_TYPE
+                        Read file type (for bowtie2; default is q=fastq; other
+                        options: qseq=solexa, f=fasta).
+  --mlst_db MLST_DB     Fasta file of MLST alleles (optional)
+  --mlst_delimiter MLST_DELIMITER
+                        Character(s) separating gene name from allele number
+                        in MLST database (default "-", as in arcc-1)
+  --mlst_definitions MLST_DEFINITIONS
+                        ST definitions for MLST scheme (required if mlst_db
+                        supplied and you want to calculate STs)
+  --mlst_max_mismatch MLST_MAX_MISMATCH
+                        Maximum number of mismatches per read for MLST allele
+                        calling (default 10)
+  --gene_db GENE_DB 
+                        Fasta file/s for gene databases (optional)
+  --no_gene_details     Switch OFF verbose reporting of gene typing
+  --gene_max_mismatch GENE_MAX_MISMATCH
+                        Maximum number of mismatches per read for gene
+                        detection and allele calling (default 10)
+  --min_coverage MIN_COVERAGE
+                        Minimum %coverage cutoff for gene reporting (default
+                        90)
+  --max_divergence MAX_DIVERGENCE
+                        Maximum %divergence cutoff for gene reporting (default
+                        10)
+  --min_depth MIN_DEPTH
+                        Minimum mean depth to flag as dubious allele call
+                        (default 5)
+  --min_edge_depth MIN_EDGE_DEPTH
+                        Minimum edge depth to flag as dubious allele call
+                        (default 2)
+  --prob_err PROB_ERR   Probability of sequencing error (default 0.01)
+  --truncation_score_tolerance TRUNCATION_SCORE_TOLERANCE
+                        % increase in score allowed to choose non-truncated
+                        allele
+  --stop_after STOP_AFTER
+                        Stop mapping after this number of reads have been
+                        mapped (otherwise map all)
+  --other OTHER        			 
+			Other arguments to pass to bowtie2 (must be escaped,
+                        e.g. "\\--no-mixed".)
+  --max_unaligned_overlap MAX_UNALIGNED_OVERLAP
+                        Read discarded from alignment if either of its ends
+                        has unaligned overlap with the reference that is
+                        longer than this value (default 10)
+  --mapq MAPQ           Samtools -q parameter (default 1)
+  --baseq BASEQ         Samtools -Q parameter (default 20)
+  --samtools_args SAMTOOLS_ARGS
+                        Other arguments to pass to samtools mpileup (must be
+                        escaped, e.g. "\\-A").
+  --output OUTPUT       Prefix for srst2 output files
+  --log                 Switch ON logging to file (otherwise log to stdout)
+  --save_scores         Switch ON verbose reporting of all scores
+  --report_new_consensus
+                        If a matching alleles is not found, report the
+                        consensus allele. Note, only SNP differences are
+                        considered, not indels.
+  --report_all_consensus
+                        Report the consensus allele for the most likely
+                        allele. Note, only SNP differences are considered, not
+                        indels.
+  --use_existing_bowtie2_sam
+                        Use existing SAM file generated by Bowtie2 if
+                        available, otherwise they will be generated
+  --use_existing_pileup
+                        Use existing pileups if available, otherwise they will
+                        be generated
+  --use_existing_scores
+                        Use existing scores files if available, otherwise they
+                        will be generated
+  --keep_interim_alignment
+                        Keep interim files (sam & unsorted bam), otherwise
+                        they will be deleted after sorted bam is created
+  --threads THREADS     Use multiple threads in Bowtie and Samtools
+  --prev_output PREV_OUTPUT 
+                        SRST2 results files to compile (any new results from
+                        this run will also be incorporated)
+
+
+    ]]></help>
+
+
+    <citations>
+        <citation type="bibtex">
+        @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014, 
+        title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs}, 
+        url={https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6}, 
+        journal={Genome Medicine}, publisher={BioMed Central}, 
+        author={Pope, Bernard J and Dashnow, Harriet and Zobel, Justin and Holt, Kathryn E and Raven, Lesley-Ann and Schultz, Mark B and Inouye, Michael and Tomita, Takehiro}, 
+        year={2014}, month={Nov}} ,
+       }</citation>
+    </citations>
+</tool>