Mercurial > repos > iuc > orthofinder_onlygroups

comparison orthofinder_only_groups.xml @ 8:f55cad755bcc 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 10:27:51 +0000
parents 63f76f6f65b3
children f03ba0ec3eed
comparison
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7:63f76f6f65b3 8:f55cad755bcc
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
11 <requirement type="package" version="2.34">util-linux</requirement> 11 <requirement type="package" version="2.36">util-linux</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 #import re 14 #import re
15 ## prepare inputs 15 ## prepare inputs
16 #if $init.start == "fasta": 16 #if $init.start == "fasta":
48 ## start Orthofinder 48 ## start Orthofinder
49 orthofinder 49 orthofinder
50 #if $init.start == "fasta": 50 #if $init.start == "fasta":
51 -f . 51 -f .
52 -S $init.search.search_program 52 -S $init.search.search_program
53 $init.input_type
53 #elif $init.start == "blast": 54 #elif $init.start == "blast":
54 -b . 55 -b .
55 #end if 56 #end if
56 57
57 -I $I 58 -I $I
80 #end if 81 #end if
81 ]]></command> 82 ]]></command>
82 <inputs> 83 <inputs>
83 <!-- Control where Orthofinder starts --> 84 <!-- Control where Orthofinder starts -->
84 <conditional name="init"> 85 <conditional name="init">
85 <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.">
86 <option value="fasta" selected="true">From fasta proteomes</option> 87 <option value="fasta" selected="true">From fasta files</option>
87 <option value="blast">From blast results</option> 88 <option value="blast">From blast results</option>
88 </param> 89 </param>
89 90
90 <when value="fasta"> 91 <when value="fasta">
91 <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>
92 <conditional name="search"> 97 <conditional name="search">
93 <param name="search_program" type="select" label="Sequence search program"> 98 <param name="search_program" type="select" label="Sequence search program">
94 <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>
95 <option value="blast">Blast</option> 101 <option value="blast">Blast</option>
96 <option value="blast_gz">Blast_gz - blast results gzipped</option> 102 <option value="blast_gz">Blast_gz - blast results gzipped</option>
97 </param> 103 </param>
98 <when value="blast"> 104 <when value="blast">
99 <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"/>
100 </when> 106 </when>
101 <when value="diamond"></when> 107 <when value="diamond"></when>
108 <when value="diamond_ultra_sens"></when>
102 <when value="blast_gz"></when> 109 <when value="blast_gz"></when>
103 </conditional> 110 </conditional>
104 </when> 111 </when>
105 112
106 <when value="blast"> 113 <when value="blast">
769 - The SequencesIDs.txt file 776 - The SequencesIDs.txt file
770 777
771 ---------- 778 ----------
772 Parameters 779 Parameters
773 ---------- 780 ----------
774 - 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)
775 - 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
776 - Inflation : the inflation parameter; modify this parameter is not recommended. 783 - Inflation : the inflation parameter; modify this parameter is not recommended.
777 784
778 </help> 785 </help>
779 <expand macro="citations"/> 786 <expand macro="citations"/>