comparison bio_hansel.xml @ 7:af59ac462926 draft

planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty
author nml
date Fri, 06 Apr 2018 14:20:32 -0400
parents 5a42e475436e
children e9fd173fc7ee
comparison
equal deleted inserted replaced
6:5a42e475436e 7:af59ac462926
1 <tool id="bio_hansel" name="Bio Hansel" version="1.2.1"> 1 <tool id="bio_hansel" name="Bio Hansel" version="1.3.0">
2 <description>SNV Subtyping with genome assemblies or reads</description> 2 <description>SNV Subtyping with genome assemblies or reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bio_hansel</requirement> 4 <requirement type="package" version="1.3.0">bio_hansel</requirement>
5 <requirement type="package" version="17.2.0">attrs</requirement> 5 <requirement type="package" version="17.2.0">attrs</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## Preparing file input. 8 ## Preparing file input.
9 #if $data_type.type == "paired": 9 #if $data_type.type == "paired":
177 <param name="type" value="single"/> 177 <param name="type" value="single"/>
178 <param name="type_of_scheme" value="heidelberg"/> 178 <param name="type_of_scheme" value="heidelberg"/>
179 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> 179 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
180 <output name="results.tab"> 180 <output name="results.tab">
181 <assert_contents> 181 <assert_contents>
182 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/> 182 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
183 </assert_contents> 183 </assert_contents>
184 </output> 184 </output>
185 <output name="match_results.tab"> 185 <output name="match_results.tab">
186 <assert_contents> 186 <assert_contents>
187 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 187 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
198 <param name="type_of_scheme" value="heidelberg"/> 198 <param name="type_of_scheme" value="heidelberg"/>
199 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/> 199 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
200 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> 200 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
201 <output name="results.tab"> 201 <output name="results.tab">
202 <assert_contents> 202 <assert_contents>
203 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path"/> 203 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
204 </assert_contents> 204 </assert_contents>
205 </output> 205 </output>
206 <output name="match_results.tab"> 206 <output name="match_results.tab">
207 <assert_contents> 207 <assert_contents>
208 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 208 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
321 321
322 ]]></help> 322 ]]></help>
323 <citations> 323 <citations>
324 <citation type="bibtex">@ARTICLE{a1, 324 <citation type="bibtex">@ARTICLE{a1,
325 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.}, 325 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
326 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.}, 326 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
327 url = {https://github.com/phac-nml/bio_hansel} 327 url = {https://github.com/phac-nml/bio_hansel}
328 } 328 }
329 }</citation> 329 }</citation>
330 </citations> 330 </citations>
331 </tool> 331 </tool>