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comparison sistr_cmd.xml @ 3:5c8ff92e38a9 draft

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Update to 1.0.2
author nml
date Wed, 14 Jun 2017 14:36:59 -0400
parents 13632190a0ff
children 17fcac7ddf54
comparison
equal deleted inserted replaced
2:13632190a0ff 3:5c8ff92e38a9
1 <tool id="sistr_cmd" name="sistr_cmd" version="0.3.6"> 1 <tool id="sistr_cmd" name="sistr_cmd" version="1.0.2">
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="0.3.6">sistr_cmd</requirement> 6 <requirement type="package" version="1.0.2">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 28 $more_output
29 $report_blast_results
30 $verbosity 29 $verbosity
31 ]]></command> 30 ]]></command>
32 <inputs> 31 <inputs>
33 <param 32 <param
34 name="input_fastas" 33 name="input_fastas"
84 truevalue="--qc" 83 truevalue="--qc"
85 falsevalue="" 84 falsevalue=""
86 label="Basic QC of results" 85 label="Basic QC of results"
87 /> 86 />
88 <param 87 <param
89 name="report_blast_results" 88 name="more_output"
90 type="boolean" 89 type="select"
91 checked="false" 90 label="Results verbosity">
92 truevalue="--report-blast-results" 91 <option value="" selected="true">
93 falsevalue="" 92 Basic results only
94 label="Report all blastn results from antigen search" 93 </option>
95 /> 94 <option value="-M">
96 <param 95 Report top antigen BLAST results
97 name="full_output" 96 </option>
98 type="boolean" 97 <option value="-MM" >
99 checked="false" 98 Report all antigen BLAST results
100 truevalue="--full-output" 99 </option>
101 falsevalue="" 100 </param>
102 label="Report detailed results"
103 />
104 <param 101 <param
105 name="keep_tmp" 102 name="keep_tmp"
106 type="boolean" 103 type="boolean"
107 checked="false" 104 checked="false"
108 falsevalue="" 105 falsevalue=""
165 <tests> 162 <tests>
166 <test> 163 <test>
167 <param name="input_fastas" value="AE014613-699860.fasta"/> 164 <param name="input_fastas" value="AE014613-699860.fasta"/>
168 <param name="output_format" value="tab"/> 165 <param name="output_format" value="tab"/>
169 <output 166 <output
170 name="novel_alleles"
171 value="novel-alleles.fasta"
172 ftype="fasta"
173 compare="sim_size"/>
174 <output
175 name="cgmlst_profiles" 167 name="cgmlst_profiles"
176 value="cgmlst-profiles.csv" 168 value="cgmlst-profiles.csv"
177 ftype="csv" 169 ftype="csv"
178 lines_diff="2"> 170 lines_diff="2">
179 <assert_contents> 171 <assert_contents>
180 <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1123870984,278162969,490843778,3950769715,,,,,,4203409135,3569491948,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,2019769394,1109678443,,,,,,,,,"/> 172 <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/>
181 </assert_contents> 173 </assert_contents>
182 </output> 174 </output>
183 <output 175 <output
184 name="output_prediction_tab" 176 name="output_prediction_tab"
185 value="sistr-results.tab" 177 value="sistr-results.tab"
265 name="alleles_output" 257 name="alleles_output"
266 value="alleles-output-13-1101.json" 258 value="alleles-output-13-1101.json"
267 ftype="json" 259 ftype="json"
268 compare="sim_size"/> 260 compare="sim_size"/>
269 </test> 261 </test>
262 <test>
263 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
264 <param name="output_format" value="json"/>
265 <param name="more_output" value="-MM"/>
266 <output
267 name="output_prediction_json"
268 value="sistr-results-13-1101.json"
269 ftype="json"
270 compare="sim_size">
271 <assert_contents>
272 <has_text text="13-1101-Paratyphi_B" />
273 <has_text text="Paratyphi B var. Java" />
274 <has_text text="enterica" />
275 <has_text text="1,4,[5],12" />
276 <has_text text="PASS" />
277 </assert_contents>
278 </output>
279 </test>
270 </tests> 280 </tests>
271 <help> 281 <help>
272 <![CDATA[ 282 <![CDATA[
273 283
274 Usage:: 284 Usage::
275 285
276 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] 286 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
277 [-o OUTPUT_PREDICTION] [--full-output] 287 [-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES]
278 [--report-blast-results] [-p CGMLST_PROFILES]
279 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] 288 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
280 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] 289 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
281 [-v] [-V] 290 [-v] [-V]
282 [F [F ...]] 291 [F [F ...]]
283 292
303 fasta file path to genome name pair 312 fasta file path to genome name pair
304 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT 313 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
305 Output format (json, csv, pickle) 314 Output format (json, csv, pickle)
306 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION 315 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
307 SISTR serovar prediction output path 316 SISTR serovar prediction output path
308 --full-output Produce full detailed output 317 -M, --more-results Output more detailed results (-M) and all antigen
309 --report-blast-results 318 search blastn results (-MM)
310 Report blastn results for each antigen gene
311 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES 319 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
312 Output CSV file destination for cgMLST allelic 320 Output CSV file destination for cgMLST allelic
313 profiles 321 profiles
314 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES 322 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
315 Output FASTA file destination of novel cgMLST alleles 323 Output FASTA file destination of novel cgMLST alleles