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comparison kobas_identify.xml @ 4:20f1b45dea63 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:50:07 -0500
parents 83b998fa34ea
children
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3:83b998fa34ea 4:20f1b45dea63
1 <tool id="kobas_identify" name="KOBAS Identify" version="@WRAPPER_VERSION@"> 1 <tool id="kobas_identify" name="KOBAS Identify" version="@TOOL_VERSION@">
2 <description>KEGG Orthology Based Annotation System</description> 2 <description>KEGG Orthology Based Annotation System</description>
3 <macros> 3 <macros>
4 <import>kobas_macros.xml</import> 4 <import>kobas_macros.xml</import>
5 </macros> 5 </macros>
6 6
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 8
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 mkdir sqlite &&
11 mkdir seq_pep &&
11 12
12 mkdir sqlite && 13 #if not isinstance( $db.value, list ):
13 mkdir seq_pep && 14 #set $db_args = [ $db.value ]
15 #else:
16 #set $db_args = $db.value
17 #end if
18 #set $db_args = "/".join($db.value)
14 19
15 #if not isinstance( $db.value, list ): 20 ln -s '$kobasdb' 'sqlite/${species}.db' &&
16 #set $db_args = [ $db.value ]
17 #else:
18 #set $db_args = $db.value
19 #end if
20 #set $db_args = "/".join($db.value)
21 21
22 ln -s '$kobasdb' 'sqlite/${species}.db' && 22 kobas-identify
23 23 -f '$fgfile'
24 kobas-identify 24 #if $bg.bgtype == 'file':
25 -f '$fgfile' 25 -b '$bg.bgfile'
26 #if $bg.bgtype == 'file': 26 #elif $bg.bgtype == 'species':
27 -b '$bg.bgfile' 27 -b '$bg.bgspecies'
28 #elif $bg.bgtype == 'species': 28 #end if
29 -b '$bg.bgspecies' 29 -d '$db_args'
30 #end if 30 -m '$method'
31 -d '$db_args' 31 -n '$fdr'
32 -m '$method' 32 -c $cutoff
33 -n '$fdr' 33 -q sqlite
34 -c $cutoff 34 -p blastp
35 -q sqlite 35 -x blastx
36 -p blastp 36 -o '$output'
37 -x blastx 37 ]]></command>
38 -o '$output'
39 ]]>
40 </command>
41 <inputs> 38 <inputs>
42 <param format="tabular" type="data" label="Foreground" argument="--fgfile" help="Foreground file, the output of KOBAS Annotate"/> 39 <param argument="--fgfile" type="data" format="tabular" label="Foreground" help="Foreground file, the output of KOBAS Annotate"/>
43 40
44 <expand macro="input_kobasdb"/> 41 <expand macro="input_kobasdb"/>
45 42
46 <param type="select" label="Database" argument="--db" multiple="True" display="checkboxes" help="Select your desired databases: 43 <param type="select" label="Database" argument="--db" multiple="True" optional="false" display="checkboxes" help="Select your desired databases:
47 (Note: the Corrected P-Values will be affected by the number of selected databases)"> 44 (Note: the Corrected P-Values will be affected by the number of selected databases)">
48 <option value="K">KEGG Pathway</option> 45 <option value="K">KEGG Pathway</option>
49 <option value="n">PID</option> 46 <option value="n">PID</option>
50 <option value="b">BioCarta</option> 47 <option value="b">BioCarta</option>
51 <option value="R">Reactome</option> 48 <option value="R">Reactome</option>
56 <option value="f">FunDo</option> 53 <option value="f">FunDo</option>
57 <option value="g">GAD</option> 54 <option value="g">GAD</option>
58 <option value="N">NHGRI GWAS Catalog</option> 55 <option value="N">NHGRI GWAS Catalog</option>
59 <option value="G">Gene Ontology</option> 56 <option value="G">Gene Ontology</option>
60 <option value="S">Gene Ontology Slim (GOslim)</option> 57 <option value="S">Gene Ontology Slim (GOslim)</option>
61 <validator type="no_options" message="You must pick at least one database."/>
62 </param> 58 </param>
63 59
64 <conditional name="bg"> 60 <conditional name="bg">
65 <param 61 <param name="bgtype" argument="--bgfile" type="select" label="Background"
66 name="bgtype"
67 type="select"
68 argument="--bgfile"
69 label="Background"
70 help="Optional background file, the output of annotate (3 or 4-letter 62 help="Optional background file, the output of annotate (3 or 4-letter
71 file name is not allowed), or species abbreviation 63 file name is not allowed), or species abbreviation
72 (for example: hsa for Homo sapiens, mmu for Mus 64 (for example: hsa for Homo sapiens, mmu for Mus
73 musculus, dme for Drosophila melanogaster, ath for 65 musculus, dme for Drosophila melanogaster, ath for
74 Arabidopsis thaliana, sce for Saccharomyces cerevisiae 66 Arabidopsis thaliana, sce for Saccharomyces cerevisiae
78 <option value="file">Background file from KOBAS Annotate</option> 70 <option value="file">Background file from KOBAS Annotate</option>
79 <option value="species">Species abbreviation</option> 71 <option value="species">Species abbreviation</option>
80 </param> 72 </param>
81 <when value="same"></when> 73 <when value="same"></when>
82 <when value="file"> 74 <when value="file">
83 <param format="txt" name="bgfile" type="data" label="Background file"/> 75 <param name="bgfile" type="data" format="txt" label="Background file"/>
84 </when> 76 </when>
85 <when value="species"> 77 <when value="species">
86 <param 78 <param name="bgspecies" type="text" label="Species abbreviation"
87 name="bgspecies"
88 type="text"
89 label="Species abbreviation"
90 help="For example: ko for KEGG 79 help="For example: ko for KEGG
91 Orthology, hsa for Homo sapiens, mmu for Mus musculus, 80 Orthology, hsa for Homo sapiens, mmu for Mus musculus,
92 dme for Drosophila melanogaster, ath for Arabidopsis 81 dme for Drosophila melanogaster, ath for Arabidopsis
93 thaliana, sce for Saccharomyces cerevisiae and eco for 82 thaliana, sce for Saccharomyces cerevisiae and eco for
94 Escherichia coli K-12 MG1655"/> 83 Escherichia coli K-12 MG1655"/>
100 <option value="b">Binomial test</option> 89 <option value="b">Binomial test</option>
101 <option value="c">Chi-square test</option> 90 <option value="c">Chi-square test</option>
102 <option value="x">Frequency list</option> 91 <option value="x">Frequency list</option>
103 </param> 92 </param>
104 93
105 <param type="select" argument="--fdr" label="FDR" help="False discovery rate (FDR) correction method"> 94 <param argument="--fdr" type="select" label="FDR" help="False discovery rate (FDR) correction method">
106 <option selected="True" value="BH">Benjamini and Hochberg</option> 95 <option selected="True" value="BH">Benjamini and Hochberg</option>
107 <option value="BY">Benjamini and Yekutieli</option> 96 <option value="BY">Benjamini and Yekutieli</option>
108 <option value="QVALUE">QVALUE</option> 97 <option value="QVALUE">QVALUE</option>
109 <option value="None">None</option> 98 <option value="None">None</option>
110 </param> 99 </param>
111 100
112 <param type="integer" min="0" argument="--cutoff" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/> 101 <param argument="--cutoff" type="integer" min="0" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/>
113
114 </inputs> 102 </inputs>
115 <outputs> 103 <outputs>
116 <data format="tabular" name="output"/> 104 <data name="output" format="tabular"/>
117 </outputs> 105 </outputs>
118 106
119 <tests> 107 <tests>
120 <test> 108 <test>
121 <param name="fgfile" value="kobas_annotate_output.txt"/> 109 <param name="fgfile" value="kobas_annotate_output.txt"/>
123 <param name="kobasdb" value="aaa.db"/> 111 <param name="kobasdb" value="aaa.db"/>
124 <param name="db" value="K"/> 112 <param name="db" value="K"/>
125 <conditional name="bg"> 113 <conditional name="bg">
126 <param name="bgtype" value="same"/> 114 <param name="bgtype" value="same"/>
127 </conditional> 115 </conditional>
128 <output name="out_file1" file="kobas_identify_output.txt"/> 116 <output name="output" file="kobas_identify_output.txt"/>
129 </test> 117 </test>
130 </tests> 118 </tests>
131 119
132 <help> 120 <help>
133 @HELP_KOBAS_INFO@ 121 @HELP_KOBAS_INFO@