comparison roary.xml @ 1:a9098353ae22 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 0c61b60404e4e1dfb5be4fb2fd310f9f3606c7a6

0:e02e9af2743f

      </conditional>
      <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
      <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"/>
      
      <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.">
        <option value="abg_fa">Accessory binary genes in fasta format</option>
        <option value="accgraph">Accessory graph in dot format</option>
        <option value="acchead_embl">Accessory header file in embl format</option>
        <option value="acctab">Accessory gene table in tabular format</option>
        <option value="blastfreq">Blast Identity Frequency Rtab file</option>

      <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" />
      <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
      <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
      <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
        <filter>outputs and 'abg_fa' in outputs</filter>
      </data>
      <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
        <filter>outputs and 'accgraph' in outputs</filter>
      </data>
      <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" >

1:a9098353ae22

      </conditional>
      <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
      <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"/>
      
      <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.">
        <option value="abg_nw">Accessory binary genes in newick format</option>
        <option value="abg_fa">Accessory binary genes in fasta format</option>
        <option value="accgraph">Accessory graph in dot format</option>
        <option value="acchead_embl">Accessory header file in embl format</option>
        <option value="acctab">Accessory gene table in tabular format</option>
        <option value="blastfreq">Blast Identity Frequency Rtab file</option>

      <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" />
      <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
      <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
      <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
        <filter>outputs and 'abg_fa' in outputs</filter>
      </data>
      <data format="nhx" name="acc_bin_new" label="${tool.name} on ${on_string} Accessory Binary Genes (Newick)" from_work_dir="out/accessory_binary_genes.fa.newick" >
        <filter>outputs and 'abg_nw' in outputs</filter>
      </data>
      <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
        <filter>outputs and 'accgraph' in outputs</filter>
      </data>
      <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" >