Mercurial > repos > rliterman > csp2

comparison csp2_snp.xml @ 32:a12953834916

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"planemo upload"
author rliterman
date Thu, 05 Dec 2024 10:47:01 -0500
parents 1fe21a8717d4
children 6f4e6377ba64
comparison
equal deleted inserted replaced
31:1117def5cd24 32:a12953834916
93 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 93 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
94 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 94 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
95 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> 95 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
96 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> 96 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
97 97
98 <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID"> 98 <collection name="snp_pipeline_output" type="list">
99 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> 99 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/CSP2_SNP_Pipeline\.log" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
100 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" /> 100 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
101 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" /> 101 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist_preserved\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
102 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" /> 102 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Reference_Screening\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
103 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> 103 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Locus_Categories\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
104 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" /> 104 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Query_Coverage\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
105 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" /> 105 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
106 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" /> 106 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
107 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" /> 107 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
108 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" /> 108 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
109 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> 109 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma_preserved\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
110 <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" /> 110 <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
111 </collection> 111 </collection>
112
112 </outputs> 113 </outputs>
113 <tests> 114 <tests>
114 <test> 115 <test>
115 <param name="query_fasta"> 116 <param name="query_fasta">
116 <collection type="list"> 117 <collection type="list">