# HG changeset patch
# User estrain
# Date 1511926503 18000
# Node ID d381880c66f12d238b45735720d316ce3c4e15c6
# Parent  0869a76e692bdfd8aab7d40719784638603c0a37
Deleted selected files

diff -r 0869a76e692b -r d381880c66f1 srst2_fda.xml
--- a/srst2_fda.xml	Tue Nov 28 22:34:44 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-<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>