Mercurial > repos > iuc > orthofinder_onlygroups

comparison orthofinder_only_groups.xml @ 7:904fb55e9156 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c"
author iuc
date Fri, 19 Nov 2021 10:29:04 +0000
parents 0ff17c7a18cd
children 3b974afde673
comparison
equal deleted inserted replaced
6:0ff17c7a18cd 7:904fb55e9156
1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>finds orthogroups in a set of proteomes</description> 2 <description>finds orthogroups in a set of proteomes</description>
3 <xrefs>
4 <xref type="bio.tools">OrthoFinder</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
8 <requirement type="package" version="2.34">util-linux</requirement> 11 <requirement type="package" version="2.36">util-linux</requirement>
9 </requirements> 12 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
11 #import re 14 #import re
12 ## prepare inputs 15 ## prepare inputs
13 #if $init.start == "fasta": 16 #if $init.start == "fasta":
45 ## start Orthofinder 48 ## start Orthofinder
46 orthofinder 49 orthofinder
47 #if $init.start == "fasta": 50 #if $init.start == "fasta":
48 -f . 51 -f .
49 -S $init.search.search_program 52 -S $init.search.search_program
53 $init.input_type
50 #elif $init.start == "blast": 54 #elif $init.start == "blast":
51 -b . 55 -b .
52 #end if 56 #end if
53 57
54 -I $I 58 -I $I
77 #end if 81 #end if
78 ]]></command> 82 ]]></command>
79 <inputs> 83 <inputs>
80 <!-- Control where Orthofinder starts --> 84 <!-- Control where Orthofinder starts -->
81 <conditional name="init"> 85 <conditional name="init">
82 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run."> 86 <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta files' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
83 <option value="fasta" selected="true">From fasta proteomes</option> 87 <option value="fasta" selected="true">From fasta files</option>
84 <option value="blast">From blast results</option> 88 <option value="blast">From blast results</option>
85 </param> 89 </param>
86 90
87 <when value="fasta"> 91 <when value="fasta">
88 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/> 92 <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta files" help="One fasta file per species; species and sequence names in the results will remain the same than in the input files."/>
93 <param name="input_type" type="select" label="Input contains nucleotide or amino acid sequences?">
94 <option value="">Amino acid</option>
95 <option value="-d">Nucleotide</option>
96 </param>
89 <conditional name="search"> 97 <conditional name="search">
90 <param name="search_program" type="select" label="Sequence search program"> 98 <param name="search_program" type="select" label="Sequence search program">
91 <option value="diamond" selected="true">Diamond (faster)</option> 99 <option value="diamond" selected="true">Diamond (faster)</option>
100 <option value="diamond_ultra_sens">Diamond ultra-sensitive</option>
92 <option value="blast">Blast</option> 101 <option value="blast">Blast</option>
93 <option value="blast_gz">Blast_gz - blast results gzipped</option> 102 <option value="blast_gz">Blast_gz - blast results gzipped</option>
94 </param> 103 </param>
95 <when value="blast"> 104 <when value="blast">
96 <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/> 105 <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/>
97 </when> 106 </when>
98 <when value="diamond"></when> 107 <when value="diamond"></when>
108 <when value="diamond_ultra_sens"></when>
99 <when value="blast_gz"></when> 109 <when value="blast_gz"></when>
100 </conditional> 110 </conditional>
101 </when> 111 </when>
102 112
103 <when value="blast"> 113 <when value="blast">
766 - The SequencesIDs.txt file 776 - The SequencesIDs.txt file
767 777
768 ---------- 778 ----------
769 Parameters 779 Parameters
770 ---------- 780 ----------
771 - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster) 781 - Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster)
772 - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files 782 - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files
773 - Inflation : the inflation parameter; modify this parameter is not recommended. 783 - Inflation : the inflation parameter; modify this parameter is not recommended.
774 784
775 </help> 785 </help>
776 <expand macro="citations"/> 786 <expand macro="citations"/>