Mercurial > repos > kkonganti > cfsan_cronology

comparison cfsan_cronology.xml @ 11:a5f31c44f8c9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
parents ddf7a172bf30
children 78a02e8cb092
comparison
equal deleted inserted replaced
10:ddf7a172bf30 11:a5f31c44f8c9
1 <tool id="cfsan_cronology" name="cronology" version="0.1.0"> 1 <tool id="cfsan_cronology" name="cronology" version="0.2.0+galaxy23.1">
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 <container type="docker">quay.io/biocontainers/nextflow:24.04.3--hdfd78af_0</container>
5 <requirement type="package" version="1.1.0">micromamba</requirement>
6 <requirement type="package">graphviz</requirement>
7 </requirements> 5 </requirements>
8 <version_command>nextflow -version</version_command> 6 <version_command>nextflow -version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
10 mkdir -p cpipes-input || exit 1; 8 mkdir -p cpipes-input || exit 1;
9 echo -e 'We attempted to create a tree and upload to microreact.org. The following is the log of that attempt\\nand contains the URL if it was successful.\\n\\n' > upload_to_microreact.txt || exit 1;
11 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
12 #import re 11 #import re
13 #if (str($input_read_type_cond.input_read_type) == "single_long"): 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
14 #for _, $unpaired in enumerate($input_read_type_cond.input): 13 #for _, $unpaired in enumerate($input_read_type_cond.input):
15 #set read1 = str($unpaired.name) 14 #set read1 = str($unpaired.name)
47 #end if 46 #end if
48 --ref_acc $refgenome 47 --ref_acc $refgenome
49 --tuspy_n $tuspy_n 48 --tuspy_n $tuspy_n
50 --fq_filename_delim '${fq_filename_delim}' 49 --fq_filename_delim '${fq_filename_delim}'
51 --fq_filename_delim_idx $fq_filename_delim_idx 50 --fq_filename_delim_idx $fq_filename_delim_idx
52 -profile kondagac; 51 -profile gxkubernetes;
53 mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 52 mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
54 mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.dnd' > /dev/null 2>&1 || exit 1; 53 mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.newick' > || exit 1;
54 cat ./cpipes-output/upload_microreact/microreact_url.txt >> upload_to_microreact.txt || exit 1;
55 ]]></command> 55 ]]></command>
56 <inputs> 56 <inputs>
57 <conditional name="input_read_type_cond"> 57 <conditional name="input_read_type_cond">
58 <param name="input_read_type" type="select" label="Select the read collection type"> 58 <param name="input_read_type" type="select" label="Select the read collection type">
59 <option value="single_long" selected="true">Single-End short reads</option> 59 <option value="single_long" selected="true">Single-End short reads</option>
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="newick" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/> 86 <data name="mashtree" format="nhx" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.newick"/>
87 <data name="microreact" format="txt" label="cronology: Tree result from microreact.org ${on_string}" from_work_dir="upload_to_microreact.txt"/>
87 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}"> 88 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
88 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" /> 89 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
89 </collection> 90 </collection>
90 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}"> 91 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
91 <discover_datasets pattern=".*\/(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" /> 92 <discover_datasets pattern=".*\/(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />