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comparison scoary.xml @ 1:77d50ec2bcf2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit 43a8ab018d2f2ab7827cfe62a8dbcf202e368e83
author iuc
date Mon, 11 Mar 2024 21:49:00 +0000
parents 42a1a5750539
children
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0:42a1a5750539 1:77d50ec2bcf2
1 <tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01"> 1 <tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">
2 <description>calculates the assocations between all genes in the accessory genome and the traits</description> 2 <description>calculates the assocations between all genes in the accessory genome and the traits</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.6.16</token> 4 <token name="@TOOL_VERSION@">1.6.16</token>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">scoary</xref>
8 </xrefs>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">scoary</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>
8 </requirements> 11 </requirements>
9 <version_command>scoary --version</version_command> 12 <version_command>scoary --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
73 <option value="P">Empirical p-value from permutations</option> 76 <option value="P">Empirical p-value from permutations</option>
74 </param> 77 </param>
75 </repeat> 78 </repeat>
76 <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" /> 79 <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />
77 <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" /> 80 <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />
78 <param name="collapse" argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/> 81 <param argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
79 <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." /> 82 <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." />
80 </section> 83 </section>
81 84
82 <!-- Output Options --> 85 <!-- Output Options -->
83 <section name="output_options" title="Output Options" expanded="true"> 86 <section name="output_options" title="Output Options" expanded="true">