Mercurial > repos > kkonganti > cfsan_cronology

comparison cfsan_cronology.xml @ 3:329a44262970

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 14:30:27 -0500
parents 408603fd75ca
children 7ac696717239
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2:408603fd75ca 3:329a44262970
1 <tool id="cfsan_cronology" name="cronology" version="0.1.0+galaxy0"> 1 <tool id="cfsan_cronology" name="cronology" version="0.1.0">
2 <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description> 2 <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="23.04">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>
72 help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/> 72 help="For any data sets downloaded from NCBI into Galaxy, change this to _reverse.fastq.gz suffix."/>
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 <param name="refgenome" optional="true" value="GCF_003516125" type="text" 75 <param name="refgenome" optional="true" value="GCF_003516125" type="text"
76 label="NCBI reference genome accession" 76 label="NCBI reference genome accession"
77 help="Is the reference genome other than <i>Cronobacter sakazakii</i>? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." /> 77 help="Is the reference genome other than Cronobacter sakazakii? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." />
78 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step" 78 <param name="tuspy_n" optional="true" value="10" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step"
79 help="These hits will be used to build a genome distance based tree for your experiment run. Default value of 2 is suitable for almost all scenarios."/> 79 help="These hits will be used to build a genome distance based tree for your experiment run. Default value of 2 is suitable for almost all scenarios."/>
80 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 80 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
81 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/> 81 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
82 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> 82 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
83 </inputs> 83 </inputs>
84 <outputs> 84 <outputs>
85 <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> 85 <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
86 <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/> 86 <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
87 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}"> 87 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
88 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" match_relative_path="true" directory="./cpipes-output/cat_unique"/> 88 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
89 </collection> 89 </collection>
90 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}"> 90 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
91 <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" match_relative_path="true" recurse="true" directory="./cpipes-output/prokka"/> 91 <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
92 </collection> 92 </collection>
93 <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}"> 93 <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
94 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" match_relative_path="true" directory="./cpipes-output/polypolish"/> 94 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" />
95 </collection> 95 </collection>
96 </outputs> 96 </outputs>
97 <tests> 97 <tests>
98 <!--Test 01: long reads--> 98 <!--Test 01: long reads-->
99 <test expect_num_outputs="2"> 99 <test expect_num_outputs="2">