Mercurial > repos > kkonganti > cfsan_cronology

comparison cfsan_cronology.xml @ 12:78a02e8cb092

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author kkonganti
date Mon, 15 Jul 2024 16:16:59 -0400
parents a5f31c44f8c9
children 1e6a6e88db16
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11:a5f31c44f8c9 12:78a02e8cb092
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 Cronobacter sakazakii? 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="2" 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="5" 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>
150 on the floppy icon and view it in your browser on your local desktop/workstation. 150 on the floppy icon and view it in your browser on your local desktop/workstation.
151 You can export the tables and plots from the downloaded MultiQC report. 151 You can export the tables and plots from the downloaded MultiQC report.
152 - Polished de novo assemblies (FASTA) for each sample. 152 - Polished de novo assemblies (FASTA) for each sample.
153 - Genome annotations (GFF) for each sample. 153 - Genome annotations (GFF) for each sample.
154 - Whole genome distance based clustering tree (Newick). 154 - Whole genome distance based clustering tree (Newick).
155 - Additional metadata useful for uploading the Newick tree into iTOL. 155 - Additional metadata useful for uploading the Newick tree into iTOL.
156 - A https://microreact.org URL stored in a TXT file. An attempt will be made to upload the tree (Newick)
157 to https://microreact.org and if successful, the URL will be retrieved and stored in this TXT file.
156 158
157 ]]></help> 159 ]]></help>
158 <citations> 160 <citations>
159 <citation type="bibtex"> 161 <citation type="bibtex">
160 @article{cronology, 162 @article{cronology,