comparison raxml.xml @ 15:ac873ecba2e8 draft

planemo upload commit 6d4b6d49afc22782142019d31fc335d7d542b307

14:4148dfdaf1cd

<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
  <requirements>
    <requirement type='package' version="8.2.4">raxml</requirement>
  </requirements>
  <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
  <command interpreter="python">raxml.py
    ## Required parameters 
    ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
    ## binary is hard-coded to the pthreads enabled raxml executable
    --binary "raxmlHPC-PTHREADS"

          <param name="extraOptions" value="required"/>
          <param name="infile" value="dna.phy"/>
          <param name="model_type" value="nucleotide"/>
          <param name="base_model" value="GTRCAT"/>
          <output name="bestTreeReq" file="RAxML_bestTree.galaxy"/>
          <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy"/>
              <assert_contents>
                <has_text_matching expression="Frog" />
              </assert_contents>
          </output>
      </test>

15:ac873ecba2e8

<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
  <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
  <requirements>
    <requirement type='package' version="8.2.4">raxml</requirement>
  </requirements>
  <command interpreter="python">raxml.py
    ## Required parameters 
    ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
    ## binary is hard-coded to the pthreads enabled raxml executable
    --binary "raxmlHPC-PTHREADS"

          <param name="extraOptions" value="required"/>
          <param name="infile" value="dna.phy"/>
          <param name="model_type" value="nucleotide"/>
          <param name="base_model" value="GTRCAT"/>
          <output name="bestTreeReq" file="RAxML_bestTree.galaxy"/>
          <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy">
              <assert_contents>
                <has_text_matching expression="Frog" />
              </assert_contents>
          </output>
      </test>