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comparison cat_bins.xml @ 2:9dfc328de6ef draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
author iuc
date Thu, 09 Mar 2023 21:00:12 +0000
parents 544343d2276f
children
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1:544343d2276f 2:9dfc328de6ef
1 <tool id="cat_bins" name="CAT bins" version="@VERSION@.1"> 1 <tool id="cat_bins" name="CAT bins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>annotate with taxonomic classification</description> 2 <description>annotate with taxonomic classification</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import re
9 #set $bin_dir = None 10 #set $bin_dir = None
10 #if len($mags) > 1: 11 #if len($mags) > 1:
11 #set $bin_dir = 'inputs' 12 #set $bin_dir = 'inputs'
12 mkdir -p $bin_dir && 13 mkdir -p $bin_dir &&
13 #for mag in $mags: 14 #for mag in $mags:
14 ln -s '$mag' $bin_dir/ && 15 #set input_identifier = re.sub('[^\s\w\-]', '_', str($mag.element_identifier))
16 ln -s '$mag' '${bin_dir}/${input_identifier}.FASTA' &&
15 #end for 17 #end for
18 #else
19 #set $bin_file = re.sub('[^\s\w\-]', '_', str($mags[0].element_identifier))
20 ln -s $mags[0] '$bin_file' &&
16 #end if 21 #end if
17 CAT 22 CAT
18 #if $bin_dir 23 #if $bin_dir
19 bins -s '.dat' -b '$bin_dir' 24 bins -s '.FASTA' -b '$bin_dir'
20 #else 25 #else
21 bin -b '$mags' 26 bin -b '$bin_file'
22 #end if 27 #end if
23 @CAT_DB@ 28 @CAT_DB@
24 @USE_INTERMEDIATES@ 29 @USE_INTERMEDIATES@
25 @CUSTOM_SETTINGS@ 30 @CUSTOM_SETTINGS@
26 @DIAMOND_OPTIONS@ 31 @DIAMOND_OPTIONS@
79 </test> 84 </test>
80 <test> 85 <test>
81 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> 86 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
82 <expand macro="test_catdb"/> 87 <expand macro="test_catdb"/>
83 <param name="select_outputs" value="bin2classification"/> 88 <param name="select_outputs" value="bin2classification"/>
84 <param name="select_outputs" value="predicted_proteins_faa"/> 89 <param name="select_outputs" value="predicted_proteins_faa"/>
90 <param name="fraction" value="0.6"/>
85 <conditional name="names"> 91 <conditional name="names">
86 <param name="add_names" value="both"/> 92 <param name="add_names" value="both"/>
87 </conditional> 93 </conditional>
88 <param name="summarise" value="classification"/> 94 <param name="summarise" value="classification"/>
89 <output name="predicted_proteins_faa"> 95 <output name="predicted_proteins_faa">
92 <has_text text="contig_4403" /> 98 <has_text text="contig_4403" />
93 </assert_contents> 99 </assert_contents>
94 </output> 100 </output>
95 <output name="orf2lca_names"> 101 <output name="orf2lca_names">
96 <assert_contents> 102 <assert_contents>
97 <has_text text="Listeria" /> 103 <has_text text="Vibrionaceae" />
98 <has_text text="Vibrio" /> 104 <has_text text="Vibrio" />
99 </assert_contents> 105 </assert_contents>
100 </output> 106 </output>
101 <output name="classification_summary"> 107 <output name="classification_summary">
102 <assert_contents> 108 <assert_contents>
103 <has_text text="Listeria" /> 109 <has_text text="Gammaproteobacteria" />
104 </assert_contents> 110 </assert_contents>
105 </output> 111 </output>
106 </test> 112 </test>
107 113
108 </tests> 114 </tests>