comparison locarna_best_subtree.xml @ 3:606440a3852d draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 5a545fc913b3a07e1452e67f66b2ca593660abdf

2:5970f6f2a36b

<tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >
  <requirements>
    <requirement type="package" version="0.1.8">graphclust-wrappers</requirement>
    <requirement type="package" version='1.8.10'>locarna</requirement>
    <requirement type="package" version='2.1'>rnaz</requirement>
    <requirement type="package" version='0.07'>perl-math-round</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>
    <![CDATA[

        'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map'
        #if str($param_type.param_type_selector) == "gclust"
             $param_type.p
            $param_type.max_diff_am
            $param_type.max_diff
            $param_type.tau

  <inputs>
    <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
    <param type="data" name="tree_file" label="trees" format="text" help="text format" />
    <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
    <param type="data" name="data_map" label="data_map" format="txt" help="text format" />


    <conditional name="param_type">
    <param name="param_type_selector" type="select" label="Choose the type of parameters">
        <option value="locarna">LocARNA defaults</option>
        <option value="gclust" selected="True">GrapClust defaults(changeable)</option>

    </when>
</conditional>

  </inputs>
  <outputs>

    <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
  </outputs>
  <tests>
    <test>
      <param name="tree_file" value="1.1.tree"/>
      <param name="center_fa_file" value="1.1.center.fa"/>
      <param name="data_map" value="data.map"/>
      <param name="tree_matrix" value="1.1.matrix.tree"/>
      <conditional name="param_type">
        <param name="iteration_num_selector" value="gclust"/>
        <param name="p" value="0.001"/>
        <param name="max_diff_am" value="50"/>
        <param name="tau" value="50"/>

3:606440a3852d

<tool id="locarna_best_subtree" name="locarna_graphclust" version="0.1.0" >
  <requirements>
    <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
    <requirement type="package" version='1.8.10'>locarna</requirement>
    <requirement type="package" version='2.1'>rnaz</requirement>
    <requirement type="package" version='0.07'>perl-math-round</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>
    <![CDATA[

        'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map' $allow_overlap
        #if str($param_type.param_type_selector) == "gclust"
             $param_type.p
            $param_type.max_diff_am
            $param_type.max_diff
            $param_type.tau

  <inputs>
    <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
    <param type="data" name="tree_file" label="trees" format="text" help="text format" />
    <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
    <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
    <param name="allow_overlap" type="boolean"  truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/>

    <conditional name="param_type">
    <param name="param_type_selector" type="select" label="Choose the type of parameters">
        <option value="locarna">LocARNA defaults</option>
        <option value="gclust" selected="True">GrapClust defaults(changeable)</option>

    </when>
</conditional>

  </inputs>
  <outputs>
    <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
  </outputs>
  <tests>
    <test>
      <param name="tree_file" value="1.1.tree"/>
      <param name="center_fa_file" value="1.1.center.fa"/>
      <param name="data_map" value="data.map"/>
      <param name="tree_matrix" value="1.1.matrix.tree"/>
      <param name="allow_overlap" value="0"/>
      <conditional name="param_type">
        <param name="iteration_num_selector" value="gclust"/>
        <param name="p" value="0.001"/>
        <param name="max_diff_am" value="50"/>
        <param name="tau" value="50"/>