comparison raxml.xml @ 7:b1e68bbe4cef draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit ca98a256623d6636805d6fbc4ff85fb7465b2f90

6:ea30d3089354

<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
    <macros>
        <token name="@TOOL_VERSION@">8.2.12</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">raxml</xref>
    </xrefs>
    <requirements>

                    help="The program will exit after computation of the starting tree" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
        <!-- REQUIRED -->
        <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
            <filter>selExtraOpts['extraOptions'] == 'required'</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
        </data>
        <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
            <filter>selExtraOpts['extraOptions'] == 'required'</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
        </data>
        <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
            <filter>selExtraOpts['extraOptions'] == 'required'</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
        </data>
        <!-- ADVANCED -->
        <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
            <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
            <!--    <filter>selExtraOpts['extraOptions'] == 'full'</filter> -->
            <!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
            <filter>not selExtraOpts['majority_rule_consensus']</filter> -->
        </data>
        <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['multiple_model'] != ''</filter>
        </data>
        <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['multiple_model'] is not None </filter>
        </data>
        <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
            <filter>selExtraOpts['bootseed'] == ''</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
            <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
            <filter>not selExtraOpts['majority_rule_consensus']</filter>
        </data>
        <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
            <filter>selExtraOpts['bootseed'] == ''</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
            <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
            <filter>not selExtraOpts['majority_rule_consensus']</filter>
        </data>
        <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['multiple_model'] is not None</filter>
        </data>
        <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        <!--
            <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
            <filter>selExtraOpts['bootseed'] == ''</filter>
            <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
            <filter>selExtraOpts['constraint_file'] is None</filter>
            <filter>selExtraOpts['groupingfile'] is None</filter>
            <filter>selExtraOpts['search_complete_random_tree'] is False</filter>
            <filter>selExtraOpts['start_tree_file'] is None</filter>
            <filter>not selExtraOpts['majority_rule_consensus'] == ''</filter>
        -->
        </data>
        <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
            <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
        </data>
        <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
            <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
        </data>
        <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter>
        </data>
        <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter>
        </data>
        <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter>
        </data>
        <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
            <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
            <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
            <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <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="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Frog" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="extraOptions" value="full"/>
            <param name="infile" value="dna.fasta"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <param name="number_of_runs" value="5"/>
            <output name="parsimonyTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Chicken" />
                </assert_contents>
            </output>
            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx" compare="re_match"/>
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Whale" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

7:b1e68bbe4cef

<tool id="raxml" name="RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>Maximum Likelihood based inference of large phylogenetic trees</description>
    <macros>
        <token name="@TOOL_VERSION@">8.2.12</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">raxml</xref>
    </xrefs>
    <requirements>

                    help="The program will exit after computation of the starting tree" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="${tool.name} on ${on_string}: Info" />
        <!-- REQUIRED -->
        <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="${tool.name} on ${on_string}: Log">
            <filter>selExtraOpts['extraOptions'] == 'required' or (selExtraOpts['extraOptions'] == "full" and selExtraOpts['rapid_bootstrap_random_seed'] == '' and selExtraOpts['bootseed'] == '' and selExtraOpts['search_algorithm'] != 'a' and selExtraOpts['search_algorithm'] != 'b' and not selExtraOpts['majority_rule_consensus'])</filter>
        </data>

        <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="${tool.name} on ${on_string}: Parsimony Tree">
            <filter>selExtraOpts['extraOptions'] != "required" or selExtraOpts['search_algorithm'] != 'a'</filter>
        </data>
        <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="${tool.name} on ${on_string}: Result">
            <filter>selExtraOpts['extraOptions'] == 'required' or (selExtraOpts['extraOptions'] == "full" and selExtraOpts['rapid_bootstrap_random_seed'] == '' and selExtraOpts['bootseed'] == '' and selExtraOpts['search_algorithm'] != 'a' and selExtraOpts['search_algorithm'] != 'b' and not selExtraOpts['majority_rule_consensus'])</filter>
        </data>
        <!-- ADVANCED -->
        <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="${tool.name} on ${on_string}: Random Tree">
            <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="${tool.name} on ${on_string}: Best-scoring ML Tree"/>

        <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="${tool.name} on ${on_string}: Best-scoring ML Tree Partitions">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['multiple_model'] is not None </filter>
        </data>

        <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="${tool.name} on ${on_string}: Result Partitions">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['multiple_model'] is not None</filter>
        </data>

        <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="${tool.name} on ${on_string}: Final Bootstrap Trees">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
            <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
        </data>
        <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="${tool.name} on ${on_string}: Bipartitions">
            <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="${tool.name} on ${on_string}: Bipartitions Branch Labels">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
        </data>
        <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="${tool.name} on ${on_string}: Strict Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter>
        </data>
        <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="${tool.name} on ${on_string}: Majority Rule Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter>
        </data>
        <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="${tool.name} on ${on_string}: Majority Rule Extended Consensus Tree">
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
            <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter>
        </data>
        <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="${tool.name} on ${on_string}: Pair-wise bipartition frequences.">
            <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="${tool.name} on ${on_string}: Per-site likelihood schores">
            <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
        <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="${tool.name} on ${on_string}: Pair-wise distances">
            <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
            <filter>selExtraOpts['extraOptions'] == "full"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <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="info">
                <assert_contents><has_text text="Overall execution time"/></assert_contents>
            </output>
            <output name="log">
                <assert_contents>
                    <has_n_columns n="2" sep=" "/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="parsimonyTree" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
            <output name="result" ftype="nhx">
                <assert_contents><has_text text="Frog"/></assert_contents>
            </output>
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text_matching expression="Frog" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="5">
            <param name="extraOptions" value="full"/>
            <param name="infile" value="dna.fasta"/>
            <param name="model_type" value="nucleotide"/>
            <param name="base_model" value="GTRCAT"/>
            <param name="number_of_runs" value="5"/>
            <output name="info">
                <assert_contents><has_text text="Overall execution time"/></assert_contents>
            </output>
            <output name="log">
                <assert_contents>
                    <has_n_columns n="2" sep=" "/>
                    <has_n_lines n="41"/>
                </assert_contents>
            </output>
            <output name="result">
                <assert_contents>
                    <has_text_matching expression="Chicken" />
                    <has_n_lines n="5"/>
                </assert_contents>
            </output>
            <output name="parsimonyTree" ftype="nhx">
                <assert_contents>
                    <has_text text="(Whale,((((Mouse,Chicken),Human),Rat),((Frog,(Carp,Loach)),Seal)),Cow);"/>
                    <has_n_lines n="5"/>
                </assert_contents>
            </output>
            <output name="bestTree" ftype="nhx">
                <assert_contents>
                    <has_text text="Whale" />
                    <has_text text="Chicken"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[