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comparison cfsan_bettercallsal.xml @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
parents 1b9de878b04a
children b90e5a7a3d4f
comparison
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10:1b9de878b04a 11:749faef1caa9
1 <tool id="cfsan_bettercallsal" name="bettercallsal" version="0.2.0+galaxy0"> 1 <tool id="cfsan_bettercallsal" name="bettercallsal" version="0.6.1">
2 <description>An automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella.</description> 2 <description>An automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="22.10">nextflow</requirement> 4 <requirement type="package" version="23.04">nextflow</requirement>
5 <requirement type="package" version="1.0.0">micromamba</requirement> 5 <requirement type="package" version="1.0.0">micromamba</requirement>
6 <requirement type="package">graphviz</requirement> 6 <requirement type="package">graphviz</requirement>
7 </requirements> 7 </requirements>
8 <version_command>nextflow -version</version_command> 8 <version_command>nextflow -version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
33 #end if 33 #end if
34 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 34 ln -sf '$pair.forward' './cpipes-input/$read_R1';
35 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 35 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
36 #end for 36 #end for
37 #end if 37 #end if
38 $__tool_directory__/0.5.0/cpipes 38 $__tool_directory__/0.6.1/cpipes
39 --pipeline bettercallsal 39 --pipeline bettercallsal
40 --input \${pwd_path}/cpipes-input 40 --input \${pwd_path}/cpipes-input
41 --output \${pwd_path}/cpipes-output 41 --output \${pwd_path}/cpipes-output
42 --fq_suffix '${input_read_type_cond.fq_suffix}' 42 --fq_suffix '${input_read_type_cond.fq_suffix}'
43 #if (str($input_read_type_cond.input_read_type) == "single_long"): 43 #if (str($input_read_type_cond.input_read_type) == "single_long"):
47 #end if 47 #end if
48 --tuspy_n $tuspy_n 48 --tuspy_n $tuspy_n
49 #if ($sourmash_cond.run == "true"): 49 #if ($sourmash_cond.run == "true"):
50 --sfhpy_fcv $sourmash_cond.sfhpy_fcv 50 --sfhpy_fcv $sourmash_cond.sfhpy_fcv
51 #end if 51 #end if
52 --bcs_db_mode $bcs_db_mode
52 --bcs_thresholds $bcs_thresholds 53 --bcs_thresholds $bcs_thresholds
53 --fq_filename_delim '${fq_filename_delim}' 54 --fq_filename_delim '${fq_filename_delim}'
54 --fq_filename_delim_idx $fq_filename_delim_idx 55 --fq_filename_delim_idx $fq_filename_delim_idx
55 -profile kondagac; 56 -profile kondagac;
56 mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 57 mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
74 help="For any data sets downloaded from NCBI into Galaxy, change this to _forward.fastq.gz suffix."/> 75 help="For any data sets downloaded from NCBI into Galaxy, change this to _forward.fastq.gz suffix."/>
75 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ" 76 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"
76 help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/> 77 help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
77 </when> 78 </when>
78 </conditional> 79 </conditional>
80 <param name="bcs_db_mode" type="select" label="Select the database mode with bettercallsal"
81 help="Refer to `Database generation` section in our manuscript: https://doi.org/10.3389/fmicb.2023.1200983">
82 <option value="snp" selected="true">per_snp_cluster</option>
83 <option value="comp">per_computed_type</option>
84 </param>
79 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step" 85 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique serotypes to retain after initial MASH screen step"
80 help="The default value of 10 is suitable for almost all scenarios."/> 86 help="The default value of 10 is suitable for almost all scenarios."/>
81 <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal" 87 <param name="bcs_thresholds" type="select" label="Enter the type of base quality thresholds to be set with bettercallsal"
82 help="The default value sets strictest thresholds that tends to filter out most of the false positive hits."> 88 help="The default value sets strictest thresholds that tends to filter out most of the false positive hits.">
83 <option value="strict" selected="true">strict</option> 89 <option value="strict" selected="true">strict</option>
171 You can export the tables and plots from the downloaded MultiQC report. 177 You can export the tables and plots from the downloaded MultiQC report.
172 178
173 ]]></help> 179 ]]></help>
174 <citations> 180 <citations>
175 <citation type="bibtex"> 181 <citation type="bibtex">
176 @misc{bettercallsal, 182 @article{bettercallsal,
177 author = {Konganti, Kranti}, 183 author = {Konganti, Kranti},
178 year = {2023}, 184 year = {2023},
185 month = {August},
179 title = {bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting}, 186 title = {bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting},
180 publisher = {Cold Spring Harbor Laboratory}, 187 journal = {Frontiers in Microbiology},
181 journal = {bioRxiv}, 188 doi = {10.3389/fmicb.2023.1200983},
182 url = {https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full}} 189 url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}}
183 </citation> 190 </citation>
184 </citations> 191 </citations>
185 </tool> 192 </tool>