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comparison srst2v2.xml @ 14:5cfca4d5291a draft default tip

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author estrain
date Tue, 28 May 2019 06:48:00 -0400
parents a2c25a81368b
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13:a2c25a81368b 14:5cfca4d5291a
96 --baseq $options.baseq 96 --baseq $options.baseq
97 #end if 97 #end if
98 #else 98 #else
99 --other "'-p \${GALAXY_SLOTS:-1}'" 99 --other "'-p \${GALAXY_SLOTS:-1}'"
100 #end if 100 #end if
101
102 ; cat *results.txt | sed s/sample/${fname}/ > cat_results.txt
101 103
102 #if $job_type.job == "mlst" 104 #if $job_type.job == "mlst"
103 ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores 105 ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores
104 #end if 106 #end if
105 107
174 </conditional> 176 </conditional>
175 177
176 </inputs> 178 </inputs>
177 179
178 <outputs> 180 <outputs>
179 <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/> 181 <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*cat_results.txt"/>
180 <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores"> 182 <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores">
181 <filter>job_type['job'] == "mlst"</filter> 183 <filter>job_type['job'] == "mlst"</filter>
182 </data> 184 </data>
183 <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores"> 185 <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores">
184 <filter> job_type['job'] == "mlst"</filter>
185 </data>
186 <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt">
187 <filter> job_type['job'] == "mlst"</filter> 186 <filter> job_type['job'] == "mlst"</filter>
188 </data> 187 </data>
189 <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores"> 188 <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores">
190 <filter>job_type['job'] == "gene"</filter> 189 <filter>job_type['job'] == "gene"</filter>
191 </data> 190 </data>