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comparison csp2_snp.xml @ 34:499342837ad7

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"planemo upload"
author rliterman
date Thu, 05 Dec 2024 15:38:54 -0500
parents 6f4e6377ba64
children 106d28c851fa
comparison
equal deleted inserted replaced
33:6f4e6377ba64 34:499342837ad7
49 export TRIM_ARG="--trim_name $trim_name"; 49 export TRIM_ARG="--trim_name $trim_name";
50 else 50 else
51 export TRIM_ARG=""; 51 export TRIM_ARG="";
52 fi; 52 fi;
53 53
54 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
55 export REF_ID_ARG="--ref_id $ref_id";
56 else
57 export REF_ID_ARG="";
58 fi;
59
60 if [[ "$rescue" == "true" ]]; then 54 if [[ "$rescue" == "true" ]]; then
61 export RESCUE_ARG="--rescue"; 55 export RESCUE_ARG="--rescue";
62 else 56 else
63 export RESCUE_ARG=""; 57 export RESCUE_ARG="";
64 fi; 58 fi;
65 59
66 if [[ "$ondemand" == "true" ]]; then 60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy1 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
67 export PROFILE_ARG="-profile csp2_galaxy1";
68 else
69 export PROFILE_ARG="-profile csp2_galaxy2";
70 fi;
71 61
72 nextflow run ${__tool_directory__}/CSP2/CSP2.nf \$PROFILE_ARG --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --n_ref $n_ref --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; 62 mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done
73 zip -r CSP2_Output.zip CSP2_SNP_Output; 63 zip -r CSP2_Output.zip CSP2_SNP_Output;
74 ]]> 64 ]]>
75 </command> 65 </command>
76 <inputs> 66 <inputs>
77 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 67 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
78 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 68 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
79 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 69 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" />
87 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 77 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
88 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 78 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
89 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 79 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
90 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 80 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
91 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 81 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
92 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
93 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 82 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
94 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 83 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
95 <param name="n_ref" type="integer" value="1" label="Number of reference isolates for CSP2 to select" optional="true" />
96 <param name="ondemand" type="boolean" value="true" label="Use -profile csp2_galaxy1 (ondemand-small queue; set to false to use csp2_galaxy2 q8cpu)" optional="true" />
97 </inputs> 84 </inputs>
98 <outputs> 85 <outputs>
86 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
87 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
99 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 88 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
100 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 89 <data name="reference_screening" format="tabular" label="Reference Screening Data" from_work_dir="Output/Reference_Screening.tsv" />
101 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> 90 <data name="csp2_log" format="txt" label="CSP2 Log" from_work_dir="Output/CSP2_SNP_Pipeline.log" />
91 <data name="snp_matrix" format="tabular" label="Preserved SNP Matrix" from_work_dir="Output/snp_distance_matrix_preserved.tsv" />
92 <data name="snp_pairwise" format="tabular" label="Preserved SNP Pairwise Distances" from_work_dir="Output/snp_distance_pairwise_preserved.tsv" />
93 <data name="snp_alignment" format="fasta" label="Preserved SNP Alignment" from_work_dir="Output/snpma_preserved.fasta" />
102 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> 94 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
103
104 <collection name="snp_pipeline_output" type="list">
105 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/CSP2_SNP_Pipeline\.log" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
106 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
107 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist_preserved\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
108 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Reference_Screening\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
109 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Locus_Categories\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
110 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Query_Coverage\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
111 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
112 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
113 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
114 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
115 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma_preserved\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
116 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
117 </collection>
118
119 </outputs> 95 </outputs>
120 <tests> 96 <tests>
121 <test> 97 <test>
122 <param name="query_fasta"> 98 <param name="query_fasta">
123 <collection type="list"> 99 <collection type="list">