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comparison csp2_screen.xml @ 50:16b103443761

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 18:30:42 -0500
parents 6aea52d80ab9
children 90e29c1ddeca
comparison
equal deleted inserted replaced
49:6aea52d80ab9 50:16b103443761
5 <requirement type="package" version="1.5.8">micromamba</requirement> 5 <requirement type="package" version="1.5.8">micromamba</requirement>
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 9
10 mkdir ./queries ./references ./output; 10 mkdir ./queries ./references;
11 11
12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
13 #for query in $query_fasta: 13 #for query in $query_fasta:
14 ln -sf ${query} ./queries/${query.element_identifier}; 14 ln -sf ${query} ./queries/${query.element_identifier};
15 #end for 15 #end for
56 else 56 else
57 export REF_ID_ARG=""; 57 export REF_ID_ARG="";
58 fi; 58 fi;
59 59
60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 && 60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
61 ls -la CSP2_Screen_Output && 61 ls -la CSP2_Screen_Output;
62 sleep 5 &&
63 ls -la CSP2_Screen_Output &&
64 cp CSP2_Screen_Output/Screening_Results.tsv CSP2_Screen_Output/Raw_MUMmer_Summary.tsv CSP2_Screen_Output/Isolate_Data.tsv output/;
65 ]]> 62 ]]>
66 </command> 63 </command>
67 <inputs> 64 <inputs>
68 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 65 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
69 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 66 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
81 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 78 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
82 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 79 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
83 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> 80 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
84 </inputs> 81 </inputs>
85 <outputs> 82 <outputs>
86 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="output/Raw_MUMmer_Summary.tsv" /> 83 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
87 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="output/Isolate_Data.tsv" /> 84 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
88 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="output/Screening_Results.tsv" /> 85 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
89 </outputs> 86 </outputs>
90 <tests> 87 <tests>
91 <test> 88 <test>
92 <param name="query_fasta"> 89 <param name="query_fasta">
93 <collection type="list"> 90 <collection type="list">