Mercurial > repos > nml > srst2
comparison srst2.xml @ 1:599a4dc309aa draft
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
author | nml |
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date | Wed, 01 Mar 2017 12:39:11 -0500 |
parents | 6f870ed59b6e |
children | e59fdf6145db |
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0:6f870ed59b6e | 1:599a4dc309aa |
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1 <tool id="srst2" name="SRST2" version="0.3.6"> | 1 <tool id="srst2" name="SRST2" version="0.3.7"> |
2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> | 2 <description>Short Read Sequence Typing for Bacterial Pathogens</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.18">samtools</requirement> | |
5 <requirement type="package" version="2.1.0">bowtie2</requirement> | |
6 <requirement type="package" version="0.1.4.6">srst2</requirement> | 4 <requirement type="package" version="0.1.4.6">srst2</requirement> |
7 <requirement type="package" version="08-07-2014">vfdb</requirement> | |
8 </requirements> | 5 </requirements> |
9 <stdio> | 6 <stdio> |
10 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> | 7 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> |
11 </stdio> | 8 </stdio> |
12 <command interpreter="perl"> | 9 <command><![CDATA[ |
13 srst2.pl \$BASE/srst2.py $bam_results $scores $pileup | 10 $__tool_directory__/srst2.pl $bam_results $scores $pileup |
14 | 11 |
15 #if $mlst_or_genedb.job_type == "mlst_only" | 12 #if $mlst_or_genedb.job_type == "mlst_only" |
16 m $txt_results $alleles | 13 m $txt_results $alleles |
17 #if ($mlst_or_genedb.allele_choice.allele_report=="all") | 14 #if ($mlst_or_genedb.allele_choice.allele_report=="all") |
18 all | 15 all |
19 #else if ($mlst_or_genedb.allele_choice.allele_report=="new") | 16 #else if ($mlst_or_genedb.allele_choice.allele_report=="new") |
20 new | 17 new |
21 #end if | 18 #end if |
22 #else if $mlst_or_genedb.job_type == "custom_only" | 19 #else if $mlst_or_genedb.job_type == "custom_only" |
23 g $genes_results $fullgenes_results | 20 g $genes_results $fullgenes_results |
24 #* | 21 #* |
25 to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed | 22 to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed |
26 make the database names an array and then join | 23 make the database names an array and then join |
27 *# | 24 *# |
28 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) | 25 #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )]) |
29 "$dbs" | 26 "$dbs" |
30 #else if $mlst_or_genedb.job_type == "vfdb_only" | 27 #else if $mlst_or_genedb.job_type == "vfdb_only" |
31 g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name | 28 g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name |
32 #else if $mlst_or_genedb.job_type == "mlst_custom" | 29 #else if $mlst_or_genedb.job_type == "mlst_custom" |
119 #end if | 116 #end if |
120 #else | 117 #else |
121 --other "'-p \${GALAXY_SLOTS:-1}'" | 118 --other "'-p \${GALAXY_SLOTS:-1}'" |
122 #end if | 119 #end if |
123 | 120 |
124 --output out | 121 --output \${PWD}/out |
125 </command> | 122 ]]></command> |
126 <inputs> | 123 <inputs> |
127 <conditional name="single_or_paired"> | 124 <conditional name="single_or_paired"> |
128 <param name="type" type="select" label="Read type"> | 125 <param name="type" type="select" label="Read type"> |
129 <option value="single">Single-end</option> | 126 <option value="single">Single-end</option> |
130 <option value="paired">Paired-end</option> | 127 <option value="paired">Paired-end</option> |
131 <option value="collection">Collection Paired-end</option> | 128 <option value="collection">Collection Paired-end</option> |
132 </param> | 129 </param> |
133 <when value="single"> | 130 <when value="single"> |
134 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> | 131 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> |
135 </when> | 132 </when> |
136 <when value="paired"> | 133 <when value="paired"> |
137 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> | 134 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> |
138 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> | 135 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> |
139 </when> | 136 </when> |
140 <when value="collection"> | 137 <when value="collection"> |
141 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" /> | 138 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" /> |
142 </when> | 139 </when> |
143 </conditional> | 140 </conditional> |
144 | 141 |
145 <conditional name="mlst_or_genedb"> | 142 <conditional name="mlst_or_genedb"> |
146 <param name="job_type" type="select" label="Job type"> | 143 <param name="job_type" type="select" label="Job type"> |
168 </when> | 165 </when> |
169 <when value="mlst_vfdb"> | 166 <when value="mlst_vfdb"> |
170 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> | 167 <param name="mlst_defs" type="data" format="tabular" label="ST definitions for MLST scheme"/> |
171 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> | 168 <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/> |
172 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> | 169 <param name="vfdb_in" type="select" label="Choose a VFDB strain"> |
173 <options from_data_table="vfdb_fasta_files" /> | 170 <options from_data_table="vfdb_fasta_files" /> |
174 </param> | 171 </param> |
175 <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."/> | 172 <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."/> |
176 <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."/> | 173 <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."/> |
177 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > | 174 <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" > |
178 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> | 175 <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator> |
250 <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter> | 247 <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter> |
251 </data> | 248 </data> |
252 </outputs> | 249 </outputs> |
253 | 250 |
254 <tests> | 251 <tests> |
255 <test> | 252 <test> |
256 <output/> | 253 <param name="type" value="collection" /> |
257 </test> | 254 <param name="fastq_collection"> |
255 <collection type="paired"> | |
256 <element name="forward" value="ERR028678_sampled_1.fastq" /> | |
257 <element name="reverse" value="ERR028678_sampled_2.fastq" /> | |
258 </collection> | |
259 </param> | |
260 <param name="job_type" value="mlst_only" /> | |
261 <param name="mlst_defs" value="ecoli.txt" /> | |
262 <param name="mlst_db" value="Escherichia_coli#1.fasta" /> | |
263 <param name="mlst_max_mismatch" value="10" /> | |
264 <param name="mlst_delim" value="-" /> | |
265 <output name="bam_results" file="ERR028678_sampled.bam" ftype="bam" lines_diff="2" /> | |
266 <output name="scores" file="ERR028678_sampled_scores.tabular" /> | |
267 <!-- Don't test pileup as it is too large of a file > 90 MB --> | |
268 <!-- <output name="pileup" file="ERR028678_sampled_pileup.tabular" />--> | |
269 <output name="alleles" file="ERR028678_sampled_alleles.fasta" /> | |
270 <output name="txt_results" file="ERR028678_sampled_text_results.tabular" /> | |
271 </test> | |
258 </tests> | 272 </tests> |
259 | 273 |
260 | 274 |
261 <help> | 275 <help> |
262 What it does | 276 What it does |
369 | 383 |
370 Philip Mabon | 384 Philip Mabon |
371 | 385 |
372 Mark Iskander | 386 Mark Iskander |
373 | 387 |
388 Eric Enns | |
389 | |
374 </help> | 390 </help> |
375 <citations> | 391 <citations> |
376 <citation type="doi">10.1128/AAC.01310-13</citation> | 392 <citation type="doi">10.1128/AAC.01310-13</citation> |
377 </citations> | 393 </citations> |
378 </tool> | 394 </tool> |