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comparison sistr_cmd.xml @ 2:13632190a0ff draft

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planemo upload commit c190273bbf3bfd1efb6e14135601d746b748daab
author nml
date Thu, 20 Apr 2017 14:33:38 -0400
parents 9d7e381dfa5a
children 5c8ff92e38a9
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1:9d7e381dfa5a 2:13632190a0ff
1 <tool id="sistr_cmd" name="sistr_cmd" version="0.3.4"> 1 <tool id="sistr_cmd" name="sistr_cmd" version="0.3.6">
2 <description> 2 <description>
3 Salmonella In Silico Typing Resource commandline tool for serovar prediction 3 Salmonella In Silico Typing Resource commandline tool for serovar prediction
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.3.4">sistr_cmd</requirement> 6 <requirement type="package" version="0.3.6">sistr_cmd</requirement>
7 </requirements> 7 </requirements>
8 <stdio> 8 <stdio>
9 <exit_code range="1:" /> 9 <exit_code range="1:" />
10 </stdio> 10 </stdio>
11 <command><![CDATA[ 11 <command><![CDATA[
23 $run_mash 23 $run_mash
24 $qc 24 $qc
25 --threads "\${GALAXY_SLOTS:-1}" 25 --threads "\${GALAXY_SLOTS:-1}"
26 -T "\${TMPDIR:-/tmp}" 26 -T "\${TMPDIR:-/tmp}"
27 $keep_tmp 27 $keep_tmp
28 $full_output
29 $report_blast_results
28 $verbosity 30 $verbosity
29 ]]></command> 31 ]]></command>
30 <inputs> 32 <inputs>
31 <param 33 <param
32 name="input_fastas" 34 name="input_fastas"
80 type="boolean" 82 type="boolean"
81 checked="true" 83 checked="true"
82 truevalue="--qc" 84 truevalue="--qc"
83 falsevalue="" 85 falsevalue=""
84 label="Basic QC of results" 86 label="Basic QC of results"
87 />
88 <param
89 name="report_blast_results"
90 type="boolean"
91 checked="false"
92 truevalue="--report-blast-results"
93 falsevalue=""
94 label="Report all blastn results from antigen search"
95 />
96 <param
97 name="full_output"
98 type="boolean"
99 checked="false"
100 truevalue="--full-output"
101 falsevalue=""
102 label="Report detailed results"
85 /> 103 />
86 <param 104 <param
87 name="keep_tmp" 105 name="keep_tmp"
88 type="boolean" 106 type="boolean"
89 checked="false" 107 checked="false"
170 <assert_contents> 188 <assert_contents>
171 <has_text text="AE014613-699860" /> 189 <has_text text="AE014613-699860" />
172 <has_text text="Typhi" /> 190 <has_text text="Typhi" />
173 <has_text text="enterica" /> 191 <has_text text="enterica" />
174 <has_text text="-:-:-" /> 192 <has_text text="-:-:-" />
175 <has_n_columns n="19" /> 193 <has_n_columns n="21" />
176 </assert_contents> 194 </assert_contents>
177 </output> 195 </output>
178 <output 196 <output
179 name="alleles_output" 197 name="alleles_output"
180 value="alleles-output.json" 198 value="alleles-output.json"
204 <has_text text="13-1101-Paratyphi_B" /> 222 <has_text text="13-1101-Paratyphi_B" />
205 <has_text text="Paratyphi B var. Java" /> 223 <has_text text="Paratyphi B var. Java" />
206 <has_text text="enterica" /> 224 <has_text text="enterica" />
207 <has_text text="1,4,[5],12" /> 225 <has_text text="1,4,[5],12" />
208 <has_text text="PASS" /> 226 <has_text text="PASS" />
209 <has_text text="2375035975"/>
210 <has_n_columns n="21" /> 227 <has_n_columns n="21" />
211 </assert_contents> 228 </assert_contents>
212 </output> 229 </output>
213 <output 230 <output
214 name="alleles_output" 231 name="alleles_output"
239 <has_text text="13-1101 Paratyphi_B" /> 256 <has_text text="13-1101 Paratyphi_B" />
240 <has_text text="Paratyphi B var. Java" /> 257 <has_text text="Paratyphi B var. Java" />
241 <has_text text="enterica" /> 258 <has_text text="enterica" />
242 <has_text text="1,4,[5],12" /> 259 <has_text text="1,4,[5],12" />
243 <has_text text="PASS" /> 260 <has_text text="PASS" />
244 <has_text text="2375035975"/>
245 <has_n_columns n="21" /> 261 <has_n_columns n="21" />
246 </assert_contents> 262 </assert_contents>
247 </output> 263 </output>
248 <output 264 <output
249 name="alleles_output" 265 name="alleles_output"
256 <![CDATA[ 272 <![CDATA[
257 273
258 Usage:: 274 Usage::
259 275
260 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] 276 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
261 [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES] 277 [-o OUTPUT_PREDICTION] [--full-output]
278 [--report-blast-results] [-p CGMLST_PROFILES]
262 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] 279 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
263 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] 280 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
264 [-v] [-V] 281 [-v] [-V]
265 [F [F ...]] 282 [F [F ...]]
266 283
286 fasta file path to genome name pair 303 fasta file path to genome name pair
287 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT 304 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
288 Output format (json, csv, pickle) 305 Output format (json, csv, pickle)
289 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION 306 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
290 SISTR serovar prediction output path 307 SISTR serovar prediction output path
308 --full-output Produce full detailed output
309 --report-blast-results
310 Report blastn results for each antigen gene
291 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES 311 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
292 Output CSV file destination for cgMLST allelic 312 Output CSV file destination for cgMLST allelic
293 profiles 313 profiles
294 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES 314 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
295 Output FASTA file destination of novel cgMLST alleles 315 Output FASTA file destination of novel cgMLST alleles