Mercurial > repos > iuc > roary

comparison roary.xml @ 1:70c9cb0e2791 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 0c61b60404e4e1dfb5be4fb2fd310f9f3606c7a6
author iuc
date Thu, 06 Jul 2017 10:30:08 -0400
parents 4a9dca0bbed3
children 9d36f948b56c
comparison
equal deleted inserted replaced
0:4a9dca0bbed3 1:70c9cb0e2791
42 </conditional> 42 </conditional>
43 <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/> 43 <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
44 <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/> 44 <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
45 45
46 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced."> 46 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced.">
47 <option value="abg_nw">Accessory binary genes in newick format</option>
47 <option value="abg_fa">Accessory binary genes in fasta format</option> 48 <option value="abg_fa">Accessory binary genes in fasta format</option>
48 <option value="accgraph">Accessory graph in dot format</option> 49 <option value="accgraph">Accessory graph in dot format</option>
49 <option value="acchead_embl">Accessory header file in embl format</option> 50 <option value="acchead_embl">Accessory header file in embl format</option>
50 <option value="acctab">Accessory gene table in tabular format</option> 51 <option value="acctab">Accessory gene table in tabular format</option>
51 <option value="blastfreq">Blast Identity Frequency Rtab file</option> 52 <option value="blastfreq">Blast Identity Frequency Rtab file</option>
73 <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" /> 74 <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" />
74 <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" /> 75 <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
75 <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" /> 76 <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
76 <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" > 77 <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
77 <filter>outputs and 'abg_fa' in outputs</filter> 78 <filter>outputs and 'abg_fa' in outputs</filter>
79 </data>
80 <data format="nhx" name="acc_bin_new" label="${tool.name} on ${on_string} Accessory Binary Genes (Newick)" from_work_dir="out/accessory_binary_genes.fa.newick" >
81 <filter>outputs and 'abg_nw' in outputs</filter>
78 </data> 82 </data>
79 <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot"> 83 <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
80 <filter>outputs and 'accgraph' in outputs</filter> 84 <filter>outputs and 'accgraph' in outputs</filter>
81 </data> 85 </data>
82 <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" > 86 <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" >